;;; 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))
    (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")))