mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-11-07 15:36:20 -05:00
8394619bac
This commit was obtained by running: ./pre-inst-env guix style without any additional argument.
417 lines
16 KiB
Scheme
417 lines
16 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
|
|
;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
|
|
;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
|
|
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
|
|
;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
|
|
;;;
|
|
;;; 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 <http://www.gnu.org/licenses/>.
|
|
|
|
(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 (guix utils)
|
|
#:use-module (gnu 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 image)
|
|
#:use-module (gnu packages lisp)
|
|
#: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 "2.1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "cypari2" version))
|
|
(sha256
|
|
(base32
|
|
"0ymc4i9y60aazscc1blivirkr1rflzz6akkmvfzyn5l7mgnlbk83"))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
(list python-cython))
|
|
(propagated-inputs
|
|
(list python-cysignals))
|
|
(inputs
|
|
(list gmp 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; so we use a beta
|
|
;; release.
|
|
(define-public python-gmpy2
|
|
(package
|
|
(name "python-gmpy2")
|
|
(version "2.1.0b1")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/aleaxit/gmpy")
|
|
(commit (string-append "gmpy2-" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97"))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
(list unzip))
|
|
(inputs
|
|
(list gmp mpfr 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
|
|
(list autoconf automake 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
|
|
(list autoconf automake libtool))
|
|
(inputs
|
|
(list 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")))
|
|
|
|
;; Sage 9.1 doesn't build with ECL 20. This won't be necessary once 9.2 is
|
|
;; released. See https://trac.sagemath.org/ticket/22191
|
|
(define-public ecl-16
|
|
(package
|
|
(inherit ecl)
|
|
(version "16.1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://common-lisp.net/project/ecl/static/files/release/ecl"
|
|
"-" version ".tgz"))
|
|
(sha256
|
|
(base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))
|
|
(patches (search-patches
|
|
"ecl-16-libffi.patch"
|
|
"ecl-16-ignore-stderr-write-error.patch"
|
|
"ecl-16-format-directive-limit.patch"))))
|
|
;; Current ECL uses LGPL 2.1+
|
|
(license license:lgpl2.0+)))
|
|
|
|
(define-public pynac
|
|
(package
|
|
(name "pynac")
|
|
(version "0.7.26")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/pynac/pynac/")
|
|
(commit (string-append "pynac-" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
(list autoconf automake libtool pkg-config))
|
|
(inputs
|
|
(list flint gmp python singular))
|
|
(synopsis "Sage fork of GiNaC")
|
|
(description "Pynac is a derivative of the C++ library GiNaC, which
|
|
allows manipulation of symbolic expressions. It currently provides the
|
|
backend for symbolic expressions in Sage. The main difference between
|
|
Pynac and GiNaC is that Pynac relies on Sage to provide the operations
|
|
on numerical types, while GiNaC depends on CLN for this purpose.")
|
|
(license license:gpl2+)
|
|
(home-page "http://pynac.org/")))
|
|
|
|
;; Sage has become upstream of the following package.
|
|
(define-public zn-poly
|
|
(package
|
|
(name "zn-poly")
|
|
(version "0.9.2")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url (string-append "https://gitlab.com/sagemath/"
|
|
"zn_poly.git/"))
|
|
(commit version)))
|
|
(file-name (git-file-name "zn_poly" version))
|
|
(sha256
|
|
(base32 "1wbc3apxcldxfcw1dnwnn7fvlfb6bwvlr8glvgv6hf79p9r2s4j0"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("python" ,python-2)))
|
|
(inputs
|
|
(list gmp))
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(replace 'configure
|
|
;; The configure script chokes on --enable-fast-install.
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(invoke "./configure"
|
|
(string-append "--prefix=" (assoc-ref outputs "out"))
|
|
"--cflags=-O3 -fPIC")))
|
|
(add-before 'build 'prepare-build
|
|
(lambda _
|
|
(setenv "CC" "gcc")
|
|
#t))
|
|
(add-after 'build 'build-so
|
|
(lambda _
|
|
(invoke "make" "libzn_poly.so")))
|
|
(add-after 'install 'install-so
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(lib (string-append out "/lib"))
|
|
(soname (string-append "libzn_poly-" ,version ".so"))
|
|
(target (string-append lib "/" soname)))
|
|
(install-file "libzn_poly.a" lib)
|
|
(install-file soname lib)
|
|
(symlink target
|
|
(string-append lib "/libzn_poly.so"))
|
|
(symlink target
|
|
(string-append lib "/libzn_poly-"
|
|
,(version-major+minor version)
|
|
".so")))
|
|
#t)))))
|
|
(synopsis "Arithmetic for polynomials over Z/NZ")
|
|
(description "zn_poly implements the arithmetic of polynomials the
|
|
coefficients of which are modular integers.")
|
|
(license (list license:gpl2 license:gpl3)) ; dual licensed
|
|
(home-page "https://gitlab.com/sagemath/zn_poly")))
|
|
|
|
(define-public brial
|
|
(package
|
|
(name "brial")
|
|
(version "1.2.8")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/BRiAl/BRiAl/")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "0qhgckd4fvbs40jw14mvw89rccv94d3df27kipd27hxd4cx7y80y"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
(list autoconf automake libtool pkg-config))
|
|
(inputs
|
|
(list boost libpng m4ri))
|
|
(arguments
|
|
;; We are missing the boost unit test framework.
|
|
`(#:tests? #f
|
|
#:configure-flags (list "--without-boost-unit-test-framework")))
|
|
(synopsis "Arithmetic of polynomials over boolean rings")
|
|
(description "BRiAl is the successor to PolyBoRi maintained by the
|
|
Sage community. Its core is a C++ library, which provides high-level data
|
|
types for Boolean polynomials and monomials, exponent vectors, as well as
|
|
for the underlying polynomial rings and subsets of the powerset of the
|
|
Boolean variables. As a unique approach, binary decision diagrams are
|
|
used as internal storage type for polynomial structures.")
|
|
(license license:gpl2+)
|
|
(home-page "https://github.com/BRiAl/BRiAl/")))
|
|
|
|
(define-public lcalc
|
|
(package
|
|
(name "lcalc")
|
|
(version "1.23")
|
|
;; The original home page of the project has disappeared, as well as
|
|
;; code hosted by the original author on Google Code. The latter has
|
|
;; been copied to gitlab.com/sagemath and purportedly contains patches
|
|
;; for a never released version 1.3, that supposedly follows 1.23.
|
|
;; We use the tarball as well as the patches hosted inside the sage
|
|
;; package system distributed with the sage tarball.
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/"
|
|
"upstream/lcalc/lcalc-1.23.tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"))
|
|
(patches (search-patches "lcalc-lcommon-h.patch"
|
|
"lcalc-default-parameters-1.patch"
|
|
"lcalc-default-parameters-2.patch"
|
|
"lcalc-using-namespace-std.patch"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:tests? #f ;no tests
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'configure)
|
|
(add-before 'build 'prepare-build
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(chdir "src")
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(substitute* "Makefile"
|
|
(("^INSTALL_DIR= /usr/local")
|
|
(string-append "INSTALL_DIR=" out))))
|
|
#t))
|
|
(add-before 'install 'make-output-dirs
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "out"))
|
|
(bin (string-append out "/bin"))
|
|
(lib (string-append out "/lib"))
|
|
(include (string-append out "/include")))
|
|
(mkdir-p bin)
|
|
(mkdir-p lib)
|
|
(mkdir-p include))
|
|
#t)))))
|
|
;; FIXME:
|
|
;; We need to add pari-gp and probably pari related patches from the
|
|
;; sage project, as well as uncomment the line setting PARI_DEFINE in
|
|
;; the Makefile to get the full functionality of this package.
|
|
;; For the time being, we hope that sage can be compiled without.
|
|
(synopsis "C++ library for L-functions")
|
|
(description "Lcalc computes L-functions, in particular the Riemann
|
|
zeta function and its twists by quadratic characters.")
|
|
(license license:gpl2+)
|
|
(home-page "https://gitlab.com/sagemath/sage")))
|
|
|
|
(define-public ratpoints
|
|
(package
|
|
(name "ratpoints")
|
|
(version "2.1.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"http://www.mathe2.uni-bayreuth.de/stoll/programs/"
|
|
"ratpoints-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
|
|
(patches
|
|
;; Taken from
|
|
;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
|
|
(search-patches "ratpoints-sturm_and_rp_private.patch"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:test-target "test"
|
|
#:make-flags
|
|
(list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))
|
|
"CCFLAGS=-fPIC")
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'configure) ;no configure script
|
|
(add-before 'install 'create-install-directories
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(mkdir-p out)
|
|
(with-directory-excursion out
|
|
(for-each (lambda (d) (mkdir-p d))
|
|
'("bin" "include" "lib"))))
|
|
#t)))))
|
|
(inputs
|
|
(list gmp))
|
|
(home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
|
|
(synopsis "Find rational points on hyperelliptic curves")
|
|
(description "Ratpoints tries to find all rational points within
|
|
a given height bound on a hyperelliptic curve in a very efficient way,
|
|
by using an optimized quadratic sieve algorithm.")
|
|
(license license:gpl2+)))
|