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;;; 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 maths)
  #: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-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+)))

;; 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 cliquer
  (package
    (name "cliquer")
    (version "1.22")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/dimpase/autocliquer")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "00gcmrhi2fjn8b246w5a3b0pl7p6haxy5wjvd9kcqib1xanz59z4"))))
    (build-system gnu-build-system)
    (native-inputs (list autoconf automake libtool))
    (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://github.com/dimpase/autocliquer")))

(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 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 "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 with L-functions")
    (description
     "Lcalc computes L-functions, in particular the Riemann zeta function and its
twists by quadratic characters.")
    (license license:gpl2+)))

(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+)))

(define-public python-memory-allocator
  (package
    (name "python-memory-allocator")
    (version "0.1.3")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "memory_allocator" version))
              (sha256
               (base32
                "0qiijpv8zr7c5rjy64i4q3rb8qhn6v4yms5mza4p86y0w4m5r00k"))))
    (build-system python-build-system)
    (propagated-inputs (list python-cython))
    (home-page "https://github.com/sagemath/memory_allocator")
    (synopsis "An extension class to allocate memory easily with cython")
    (description "An extension class to allocate memory easily with cython")
    (license license:gpl3)))

(define-public python-pplpy
  (package
    (name "python-pplpy")
    (version "0.8.7")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "pplpy" version))
              (sha256
               (base32
                "1gfq5czkqxl395k06s77zij3xv7maiwagjvzmrpraxhsmvsd02sh"))))
    (build-system python-build-system)
    (inputs (list gmp
                  mpc
                  mpfr
                  pari-gp
                  ppl
                  python-cysignals
                  python-gmpy2))
    (native-inputs (list python-cython))
    (home-page "https://gitlab.com/videlec/pplpy")
    (synopsis "Python PPL wrapper")
    (description
     "This Python module pplpy provides a wrapper to the C++ Parma Polyhedra
Library (PPL).")
    (license license:gpl3)))

debug log:

solving 335d98d9f4 ...
found 335d98d9f4 in https://yhetil.org/guix-patches/4b6d43aae30a919993773f511c6097b0268a3c53.1658595756.git.guix@ikherbers.com/ ||
	https://yhetil.org/guix-patches/02d359414dd0b7091c5875ae37f4a2adfe466584.1659973115.git.guix@ikherbers.com/
found 2e9de70e4a in https://yhetil.org/guix-patches/612568de06686815affc8ea7eaa12523e53e9ca1.1659973115.git.guix@ikherbers.com/ ||
	https://yhetil.org/guix-patches/9e76f5f7308040e7e28ab6643eabe5be55674876.1658595756.git.guix@ikherbers.com/
found 1237ff8e04 in https://yhetil.org/guix-patches/8fad623072b4075781f6936fd1a324950886023c.1658595756.git.guix@ikherbers.com/ ||
	https://yhetil.org/guix-patches/55e1d58de2c6d3109c1c6e33644cefe8fb122f49.1659973115.git.guix@ikherbers.com/
found b29620a946 in https://yhetil.org/guix-patches/a92553c08f12f536582ab3a4ea5bf914c94ed38c.1658595756.git.guix@ikherbers.com/ ||
	https://yhetil.org/guix-patches/66b99e72c66e3aed984b5c48c3d8d95f86987f2c.1659973115.git.guix@ikherbers.com/
found 75720f31a5 in https://yhetil.org/guix-patches/3cf16c89d261aae63fbf9b4965e1b676d76e9609.1658595756.git.guix@ikherbers.com/ ||
	https://yhetil.org/guix-patches/786a15803950a03fa7f47abe8e3457c4d7d611f4.1659973115.git.guix@ikherbers.com/
found 7f76f8912b in https://git.savannah.gnu.org/cgit/guix.git
preparing index
index prepared:
100644 7f76f8912bf832d37a388b349680a09efe665e1c	gnu/packages/sagemath.scm

applying [1/5] https://yhetil.org/guix-patches/3cf16c89d261aae63fbf9b4965e1b676d76e9609.1658595756.git.guix@ikherbers.com/
diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 7f76f8912b..75720f31a5 100644

Checking patch gnu/packages/sagemath.scm...
Applied patch gnu/packages/sagemath.scm cleanly.

skipping https://yhetil.org/guix-patches/786a15803950a03fa7f47abe8e3457c4d7d611f4.1659973115.git.guix@ikherbers.com/ for 75720f31a5
index at:
100644 75720f31a5c3a883634505a32a3a0e9a2bd5dd10	gnu/packages/sagemath.scm

applying [2/5] https://yhetil.org/guix-patches/a92553c08f12f536582ab3a4ea5bf914c94ed38c.1658595756.git.guix@ikherbers.com/
diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 75720f31a5..b29620a946 100644

Checking patch gnu/packages/sagemath.scm...
Applied patch gnu/packages/sagemath.scm cleanly.

skipping https://yhetil.org/guix-patches/66b99e72c66e3aed984b5c48c3d8d95f86987f2c.1659973115.git.guix@ikherbers.com/ for b29620a946
index at:
100644 b29620a94640e513c7ecccf3acf3cb7eb9daca1d	gnu/packages/sagemath.scm

applying [3/5] https://yhetil.org/guix-patches/8fad623072b4075781f6936fd1a324950886023c.1658595756.git.guix@ikherbers.com/
diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index b29620a946..1237ff8e04 100644

Checking patch gnu/packages/sagemath.scm...
Applied patch gnu/packages/sagemath.scm cleanly.

skipping https://yhetil.org/guix-patches/55e1d58de2c6d3109c1c6e33644cefe8fb122f49.1659973115.git.guix@ikherbers.com/ for 1237ff8e04
index at:
100644 1237ff8e04699999469b83a8824afc166833c4fe	gnu/packages/sagemath.scm

applying [4/5] https://yhetil.org/guix-patches/612568de06686815affc8ea7eaa12523e53e9ca1.1659973115.git.guix@ikherbers.com/
diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 1237ff8e04..2e9de70e4a 100644

Checking patch gnu/packages/sagemath.scm...
Applied patch gnu/packages/sagemath.scm cleanly.

skipping https://yhetil.org/guix-patches/9e76f5f7308040e7e28ab6643eabe5be55674876.1658595756.git.guix@ikherbers.com/ for 2e9de70e4a
index at:
100644 2e9de70e4abc23c6b32e0da8186910bc19aaf2eb	gnu/packages/sagemath.scm

applying [5/5] https://yhetil.org/guix-patches/4b6d43aae30a919993773f511c6097b0268a3c53.1658595756.git.guix@ikherbers.com/
diff --git a/gnu/packages/sagemath.scm b/gnu/packages/sagemath.scm
index 2e9de70e4a..335d98d9f4 100644

Checking patch gnu/packages/sagemath.scm...
Applied patch gnu/packages/sagemath.scm cleanly.

skipping https://yhetil.org/guix-patches/02d359414dd0b7091c5875ae37f4a2adfe466584.1659973115.git.guix@ikherbers.com/ for 335d98d9f4
index at:
100644 335d98d9f4b0c2cf83d88d668f74e6fb0e9939a3	gnu/packages/sagemath.scm

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