;;; 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>
;;; Copyright © 2024 Vinicius Monego <monego@posteo.net>
;;;
;;; 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 pyproject)
#: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 check)
#:use-module (gnu packages compression)
#:use-module (gnu packages image)
#:use-module (gnu packages maths)
#:use-module (gnu packages lisp)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-xyz))
(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 "2.0.5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://gitlab.com/sagemath/lcalc")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1rwyx292y3jbsp88wagn9nhl9z7wsnl2yrs5imxkbxq87pnrj5a7"))))
(build-system gnu-build-system)
(arguments
(list #:configure-flags '(list "--with-pari")))
(inputs (list pari-gp))
(native-inputs (list autoconf automake libtool pkg-config gengetopt))
(home-page "https://gitlab.com/sagemath/lcalc")
(synopsis "C++ library for computing with L-functions")
(description
"Lcalc computes L-functions, in particular the Riemann zeta function,
Dirichlet L-functions and L-functions attached to elliptic curves and
modular forms.")
(license license:gpl2+)))
(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")))
(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 python-gmpy2
(package
(name "python-gmpy2")
(version "2.1.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "gmpy2" version))
(sha256
(base32
"1lc29g3s4z5f1qbsc2x9i9sf6wrpni9pwiwmb1wwx3hjr85i8xfs"))))
(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 python-memory-allocator
(package
(name "python-memory-allocator")
(version "0.1.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "memory_allocator" version))
(sha256
(base32 "1r7g175ddbpn5kjgs6f09s7mfachzw94p02snki6f6830dmj22fn"))))
(build-system pyproject-build-system)
(native-inputs
(list python-cython python-setuptools python-wheel))
(home-page "https://github.com/sagemath/memory_allocator")
(synopsis "Extension class to allocate memory easily with Cython")
(description "This package provides a single extension class
@code{MemoryAllocator} with @{cdef} methods
@itemize
@item @code{malloc}
@item @code{calloc}
@item @code{allocarray}
@item @code{realloc}
@item @code{reallocarray}
@item @code{aligned_malloc}
@item @code{aligned_malloc}
@item @code{aligned_calloc}
@item @code{aligned_allocarray}")
(license license:gpl3+)))
(define-public python-pplpy
(package
(name "python-pplpy")
(version "0.8.10")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pplpy" version))
(sha256
(base32 "1zggfj09zkfcabcsasq27vwbhdmkig4yn380gi6wykcih9n22anl"))))
(build-system pyproject-build-system)
(native-inputs (list python-cython-3 python-pytest))
(inputs (list gmp mpc mpfr pari-gp ppl))
(propagated-inputs (list python-cysignals python-gmpy2))
(home-page "https://github.com/sagemath/pplpy")
(synopsis "Python PPL wrapper")
(description "This Python package provides a wrapper to the C++ Parma
Polyhedra Library (PPL).")
(license license:gpl3+)))
(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+)))
;; 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")))
