;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Andreas Enge
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see .
(define-module (gnu packages sagemath)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bdw-gc)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages graph)
#:use-module (gnu packages lisp)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz))
(define-public python-cypari2
(package
(name "python-cypari2")
(version "2.1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cypari2" version))
(sha256
(base32
"1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz"))))
(build-system python-build-system)
(native-inputs
`(("python-cython" ,python-cython)))
(propagated-inputs
`(("python-cysignals" ,python-cysignals)))
(inputs
`(("gmp" ,gmp)
("pari-gp", pari-gp)))
(home-page "https://cypari2.readthedocs.io/")
(synopsis
"Python interface to the number theory library libpari")
(description
"Cypari2 provides a Python interface to the number theory library
PARI/GP. It has been spun off from the SageMath mathematics software system,
but it can be used independently.")
(license license:gpl2+)))
(define-public python2-cypari2
(package-with-python2 python-cypari2))
;; The stable version of the following package is not young enough to be
;; used with Sage, since it does not support cython. One would need to
;; use an alpha release. On the other hand, Sage can be built without it.
(define-public python-gmpy2
(package
(name "python-gmpy2")
(version "2.0.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "gmpy2" version ".zip"))
(sha256
(base32
"0grx6zmi99iaslm07w6c2aqpnmbkgrxcqjrqpfq223xri0r3w8yx"))))
(build-system python-build-system)
(native-inputs
`(("unzip" ,unzip)))
(inputs
`(("gmp" ,gmp)
("mpfr" ,mpfr)
("mpc" ,mpc)))
(home-page "https://github.com/aleaxit/gmpy")
(synopsis
"GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x")
(description
"This package provides a Python interface to the GNU multiprecision
libraries GMO, MPFR and MPC.")
(license license:lgpl3+)))
(define-public python2-gmpy2
(package-with-python2 python-gmpy2))
(define-public cliquer
(package
(name "cliquer")
(version "1.21")
;; The original source package is available from the home page and
;; has not seen any release since 2010; it comes with only a Makefile
;; without an "install" target. Instead, there is an autotoolized
;; tarball available from the Sage project.
(source
(origin
(method url-fetch)
(uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
(sha256
(base32
"1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
(build-system gnu-build-system)
(synopsis "C routines for finding cliques in weighted graphs")
(description "Cliquer is a set of reentrant C routines for finding
cliques in a weighted or unweighted graph. It uses an exact
branch-and-bound algorithm. It can search for maximum or maximum-weight
cliques or cliques with size or weight within a given range, restrict the
search to maximal cliques, store cliques in memory and call a user-defined
function for every found clique.")
(license license:gpl2+)
(home-page "https://users.aalto.fi/~pat/cliquer.html")))
(define-public libbraiding
(package
(name "libbraiding")
(version "1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url (string-append "https://github.com/miguelmarco/"
name))
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)))
(synopsis "Computations with braid groups")
(description "libbraiding performs computations with braid groups,
in particular it computes normal forms of group elements.")
(license license:gpl2+)
(home-page "https://github.com/miguelmarco/libbraiding")))
(define-public libhomfly
(package
(name "libhomfly")
(version "1.02r6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url (string-append "https://github.com/miguelmarco/"
name))
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
(build-system gnu-build-system)
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)))
(inputs
`(("libgc" ,libgc)))
(synopsis "Computation of homfly polynomials of links")
(description "libhomfly computes homfly polynomials of links,
represented as strings.")
(license license:public-domain)
(home-page "https://github.com/miguelmarco/libhomfly")))
(define-public sage
(package
(name "sage")
(version "8.6")
(source (origin
(method url-fetch)
(uri (string-append
"ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-"
version ".tar.gz"))
(sha256
(base32
"1ylpd0ziln50bfghqkgbn1n4gd7w2hl8g1gvg94igkbrknahjb44"))
(modules '((guix build utils)))
(snippet '(begin (delete-file-recursively "upstream")
(delete-file-recursively ".git")
#t))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
(add-before 'build 'setup
(lambda _
(setenv "SAGE_ROOT" (getcwd))
(setenv "SAGE_LOCAL" (getcwd))
(setenv "SAGE_SHARE" (string-append (getcwd) "/share"))
(setenv "PATH" (string-append (getcwd) "/build/bin:" (getcwd) "/src/bin:" (getenv "PATH")))
(setenv "SAGE_NUM_THREADS" "4")
(mkdir-p "var/lib/sage/installed")
(chdir "src")
#t)))))
(inputs
`(("boost" ,boost)
("cliquer" ,cliquer)
("ecl" ,ecl)
("edge-addition-planarity-suite" ,edge-addition-planarity-suite)
("flint" ,flint)
("gap" ,gap)
; ("givaro" ,givaro)
("glpk" ,glpk)
("gmp" ,gmp)
("gsl" ,gsl)
("libbraiding" ,libbraiding)
("libgc" ,libgc)
("libhomfly" ,libhomfly)
("mpc" ,mpc)
("ntl" ,ntl)
("pari-gp" ,pari-gp)
("python-cypari2" ,python2-cypari2)
("python-numpy" ,python2-numpy)
("python-six" ,python2-six)
("rw" ,rw)
("singular" ,singular)))
(native-inputs
`(("cython" ,python2-cython)
("pkg-config" ,pkg-config)
("python-cysignals" ,python2-cysignals)
("python-pkgconfig" ,python2-pkgconfig)
("python-jinja2" ,python2-jinja2)))
(synopsis "SageMath computer algebra system")
(description
"SageMath is a mathematics software built on top of many existing
packages such as NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT,
R and others. Their combined power may be accessed through a common,
Python-based language or directly via interfaces or wrappers.")
;; documentation under cc-by-sa3.0, bundled packages under various
;; other licenses, see COPYING.txt in the distribution
(license license:gpl3)
(home-page "https://www.sagemath.org/")))