;;; 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 © 2023 vicvbcun <guix@ikherbers.com>
;;;
;;; 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 copy)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (guix build-system pyproject)
  #:use-module (guix build-system trivial)
  #:use-module (guix download)
  #:use-module (guix gexp)
  #: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 base)
  #:use-module (gnu packages bdw-gc)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages commencement)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages freedesktop)
  #:use-module (gnu packages gd)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages guile)
  #:use-module (gnu packages image)
  #:use-module (gnu packages lisp)
  #:use-module (gnu packages m4)
  #: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-science)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages sqlite))


(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 cliquer
  (package
    (name "cliquer")
    (version "1.22")
    ;; 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, we use an autotoolized
    ;; fork
    (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://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 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 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 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 sagemath-data-combinatorial-designs
  (package
    (name "sagemath-data-combinatorial-designs")
    (version "20140630")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sagemath/spkg/upstream/combinatorial_designs/combinatorial_designs-"
                    version ".tar.bz2"))
              (sha256
               (base32
                "0bj8ngiq59hipa6izi6g5ph5akmy4cbk0vlsb0wa67f7grnnqj69"))))
    (build-system copy-build-system)
    (arguments
     '(#:install-plan '(("." "share/combinatorial_designs/"))))
    (home-page "https://www.sagemath.org")
    (synopsis "Data for Combinatorial Designs")
    (description
     "This package data for combinatorial designs.  It currently contains:

@itemize
@item The table of @acronym{MOLS, Mutually orthogonal Latin squares} from the
Handbook of Combinatorial Designs, 2ed.
@end itemize")
    (license license:public-domain)))

(define-public sagemath-data-conway-polynomials
  (let
      ((install-py
        (origin
          (method url-fetch)
          (uri
           "https://raw.githubusercontent.com/sagemath/sage/9.8/build/pkgs/conway_polynomials/spkg-install.py")
          (sha256 (base32
                   "1bwnqasnyv793hxg29viing4dnliz29grkhldsirq19d509yk1fs")))))
    (package
      (name "sagemath-data-conway-polynomials")
      (version "0.5")
      (source (origin
                (method url-fetch)
                (uri (string-append
                      "mirror://sagemath/spkg/upstream/conway_polynomials/conway_polynomials-"
                      version ".tar.bz2"))
                (sha256
                 (base32
                  "05zb1ly9x2bbscqv0jgc45g48xx77mfs7qdbqhn4ihmihn57iwnq"))))
      (build-system trivial-build-system)
      (arguments
       (list #:modules '((guix build utils))
             #:builder #~(begin
                           (use-modules (guix build utils))

                           (setenv "PATH"
                                   (string-join (list #+(file-append bzip2 "/bin")
                                                      #+(file-append tar "/bin")
                                                      #+(file-append python "/bin"))
                                                ":"))
                           ;; the output directory
                           (setenv "SAGE_SHARE" (string-append #$output "/share"))
                           (setenv "PYTHONPATH" (getcwd))

                           (invoke "tar" "-xvf" #$source)
                           (symlink (string-append "conway_polynomials-" #$version) "src")
                           (invoke "python3" #$install-py))))
      (home-page
       "https://www.math.rwth-aachen.de/~Frank.Luebeck/data/ConwayPol/index.html")
      (synopsis "Tables of Conway polynomials over finite fields")
      (description synopsis)
      (license #f))))

(define-public sagemath-data-elliptic-curves
  (let
      ((install-py-origin
        (origin
          (method url-fetch)
          (uri
           "https://raw.githubusercontent.com/sagemath/sage/9.8/build/pkgs/elliptic_curves/spkg-install.py")
          (sha256 (base32
                   "116g684i6mvs11fvb6fzfsr4fn903axn31vigdyb8bgpf8l4hvc5")))))
    (package
      (name "sagemath-data-elliptic-curves")
      (version "0.8.1")
      (source (origin
                (method url-fetch)
                (uri (string-append
                      "mirror://sagemath/spkg/upstream/elliptic_curves/elliptic_curves-"
                      version ".tar.bz2"))
                (sha256
                 (base32
                  "0l7xh4abw5sb4d37r0ylr3vwb88fpx2zrvfm5ql0c7yrv5q59fjz"))))
      (build-system trivial-build-system)
      (arguments
       (list #:modules '((guix build utils))
             #:builder #~(begin
                           (use-modules (guix build utils))

                           (setenv "PATH"
                                   (string-join (list #+(file-append bzip2 "/bin")
                                                      #+(file-append tar "/bin")
                                                      #+(file-append python "/bin"))
                                                ":"))
                           ;; the output directory
                           (setenv "SAGE_SHARE" (string-append #$output "/share"))
                           (setenv "PYTHONPATH" (getcwd))

                           (invoke "tar" "-xvf" #$source)
                           (symlink (string-append "elliptic_curves-" #$version) "src")
                           (invoke "python3" (assoc-ref %build-inputs "install-py")))))
      (inputs `(("install-py" ,install-py-origin)))
      (home-page "https://johncremona.github.io/ecdata/")
      (synopsis "Databases of elliptic curves")
      (description synopsis)
      (license #f))))

(define-public sagemath-data-graphs
  (package
    (name "sagemath-data-graphs")
    (version "20210214")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sagemath/spkg/upstream/graphs/graphs-" version
                    ".tar.bz2"))
              (sha256
               (base32
                "0h9p5wrxips51x6vpfiiaqzp9j004nwppzc9qc2iaqakk06pq8q7"))))
    (build-system copy-build-system)
    (arguments
     '(#:install-plan '(("." "share/graphs"))))
    (home-page "https://www.sagemath.org")
    (synopsis "Database of graphs")
    (description
     "This package contains databases of graphs.  It also includes the
@acronym{ISGCI, Information System on Graph Classes and their Inclusions}
database.")
    (license #f)))

(define-public sagemath-data-polytopes-db
  (package
    (name "sagemath-data-polytopes-db")
    (version "20170220")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sagemath/spkg/upstream/polytopes_db/polytopes_db-"
                    version ".tar.bz2"))
              (sha256
               (base32
                "1q0cd811ilhax4dsj9y5p7z8prlalqr7k9mzq178c03frbgqny6b"))))
    (build-system copy-build-system)
    (arguments
     '(#:install-plan '(("." "share/reflexive_polytopes"))))
    (home-page "https://www.sagemath.org")
    (synopsis "Lists of 2- and 3-dimensional reflexive polytopes")
    (description synopsis)
    (license #f)))

(define-public python-sagemath-standard
  (package
    (name "python-sagemath-standard")
    (version "10.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/sagemath/sage")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "01nfpp3zh43kil7pqyrdvxyawmny0sc656kbg833c2l1y6iwppyc"))))
    (build-system pyproject-build-system)
    (arguments
     (list #:tests? #f               ; tests are run in the `sagemath' package
           #:phases
           #~(modify-phases %standard-phases
               (add-after 'unpack 'prepare-build
                 (lambda _
                   (setenv "SAGE_NUM_THREADS"
                           (number->string (parallel-job-count)))
                   (setenv "SAGE_VENV" #$output)

                   (setenv "PYTHONPATH" (string-append (getcwd) "/pkgs/sage-setup"))

                   ;; broken symlink we don't need
                   (delete-file "pkgs/sage-conf/bin/sage-env-config")
                   (delete-file "pkgs/sage-conf_pypi/sage_root/configure")

                   ;; Run this before 'ensure-no-mtimes-pre-1980 so that there
                   ;; are no broken symlinks
                   (with-directory-excursion "build/pkgs/sagelib"
                     (let
                         ((original-path (getenv "PATH")))
                       (setenv "PATH" (string-append original-path ":../../bin"))
                       (invoke "sh" "./bootstrap")
                       (setenv "PATH" original-path)))))
               (add-before 'build 'cd-to-src
                 (lambda _
                   (chdir "pkgs/sagemath-standard")))
               ;; `setuptools' replaces shebangs that match `#!.*python.*' by
               ;; the intepreter running it.  Unfortunately this also matches
               ;; `sage-python'.  But using `sage-python' prevents a weird bug
               ;; where python's `multiprocessing.resource_tracker' would
               ;; execute `sage-runtests' instead of `python'.
               (add-after 'install 'fix-shebangs
                 (lambda _
                   (let*
                       ((bin (string-append #$output "/bin"))
                        (sage-python (string-append bin "/sage-python")))
                     (substitute* (find-files bin
                                              ;; don't touch these to prevent cycles
                                              ;; sage-num-threads.py -> sage-env -> sage
                                              ;; sage-venv-config -> sage-python -> sage
                                              (negate
                                               (file-name-predicate (string-join '("^sage-coverage$"
                                                                                   "^sage-num-threads\\.py$"
                                                                                   "^sage-venv-config$")
                                                                                 "|"))))
                       ;; be careful that we don't substitute the newline
                       ;; character
                       (("^#!.*python-toolchain[^\n]*") (string-append "#!" sage-python))))))
               (add-after 'install 'remove-unnecessary-scripts
                 (lambda _
                   (for-each
                    delete-file
                    (find-files (string-append #$output "/bin") "^sage-rebase"))))
               (replace 'wrap
                 (lambda* (#:key inputs #:allow-other-keys)
                   (let*
                       ((python-path (search-path-as-string->list (getenv "GUIX_PYTHONPATH")))
                        (python (dirname (search-input-file inputs "/bin/python3")))
                        (coreutils (dirname (search-input-file inputs "/bin/readlink")))
                        (sed (dirname (search-input-file inputs "/bin/sed")))
                        (xdg-open (dirname (search-input-file inputs "/bin/xdg-open")))
                        (maxima-version #$(package-version (this-package-input "maxima")))
                        (maxima-fas (search-input-file inputs
                                                       (string-append "/lib/maxima/"
                                                                      maxima-version
                                                                      "/binary-ecl/maxima.fas")))
                        (combinatorial-design (search-input-directory inputs "/share/combinatorial_designs"))
                        (conway-polynomials (search-input-directory inputs "/share/conway_polynomials"))
                        (ellcurve (search-input-directory inputs "/share/ellcurves"))
                        (cremona-mini (search-input-directory inputs "/share/cremona"))
                        (graphs (search-input-directory inputs "/share/graphs"))
                        (polytope (search-input-directory inputs "/share/reflexive_polytopes"))
                        (gap-lib (search-input-directory inputs "/lib/gap"))
                        (gap-share (search-input-directory inputs "/share/gap")))
                     ;; wrap everything possible, all things with shebang
                     ;; #!*/sage-* are still covered, as sage-* itself will be
                     ;; wrapped
                     (for-each
                      (lambda (file)
                        (false-if-exception
                         (wrap-script file
                           `("GUIX_PYTHONPATH" = ,python-path)
                           `("PATH" prefix (,(string-append #$output "/bin") ,coreutils ,python ,sed ,xdg-open))
                           `("MAXIMA_FAS" = (,maxima-fas))
                           `("COMBINATORIAL_DESIGN_DATA_DIR" = (,combinatorial-design))
                           `("CONWAY_POLYNOMIALS_DATA_DIR" = (,conway-polynomials))
                           `("ELLCURVE_DATA_DIR" = (,ellcurve))
                           `("CREMONA_MINI_DATA_DIR" = (,cremona-mini))
                           `("GRAPHS_DATA_DIR" = (,graphs))
                           `("POLYTOPE_DATA_DIR" = (,polytope))
                           `("GAP_LIB_DIR" = (,gap-lib))
                           `("GAP_SHARE_DIR" = (,gap-share)))))
                      (find-files (string-append #$output "/bin")))))))))
    (inputs (list arb
                  boost
                  brial
                  cliquer
                  coreutils
                  edge-addition-planarity-suite
                  gd
                  givaro
                  glpk
                  gmp
                  guile-3.0             ; for wrap-script
                  iml
                  libbraiding
                  libhomfly
                  linbox
                  m4ri
                  m4rie
                  mpc
                  mpfi
                  python-cypari2
                  python-gmpy2
                  python-jinja2
                  python-jupyter-core
                  python-memory-allocator
                  python-numpy
                  python-pplpy
                  rw
                  sagemath-data-combinatorial-designs
                  sagemath-data-conway-polynomials
                  sagemath-data-elliptic-curves
                  sagemath-data-graphs
                  sagemath-data-polytopes-db
                  sed
                  symmetrica
                  xdg-utils
                  zlib))
    (native-inputs (list m4 pkg-config python-cython))
    (propagated-inputs (list cddlib
                             ecl        ; also buildtime
                             eclib      ; also buildtime
                             flint      ; also buildtime
                             gap        ; also buildtime
                             gfan
                             giac       ; also buildtime
                             gmp-ecm    ; also buildtime
                             gsl        ; also buildtime
                             lcalc      ; also buildtime
                             maxima
                             mpfr
                             nauty
                             ntl        ; also buildtime
                             openblas   ; also buildtime
                             palp
                             pari-gp    ; also buildtime
                             pkg-config ; also buildtime (native)
                             python-fpylll
                             python-ipython
                             python-ipywidgets
                             python-lrcalc
                             python-networkx
                             python-pkgconfig
                             python-primecountpy
                             python-scipy
                             python-sympy
                             singular   ; also buildtime
                             sqlite
                             sympow
                             tachyon))
    (home-page "https://www.sagemath.org")
    (synopsis "Python-based computer algebra system")
    (description
     "SageMath is a free open-source mathematics software system licensed
under the GPL.  It builds on top of many existing open-source packages: NumPy,
SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.  Access their
combined power through a common, Python-based language or directly via
interfaces or wrappers.")
    (license license:gpl3)))

(define-public sagemath
  (package
    (inherit python-sagemath-standard)
    (name "sagemath")
    (arguments
     (list #:phases #~(modify-phases %standard-phases
                        (add-after 'unpack 'prepare
                          (lambda _
                            (setenv "HOME" (string-append (getenv "TMPDIR") "/home"))
                            (mkdir-p (getenv "HOME"))
                            (chdir "src")

                            ;; prevent paging for `sage/repl/ipython_tests.py'
                            (setenv "TERM" "dumb")

                            ;; for `sage --sh' in `sage/tests/cmdline.py'
                            (setenv "SHELL" (which "bash"))

                            (for-each
                             delete-file
                             '("sage/repl/ipython_kernel/install.py" ; needs threejs

                               ;; works in a container
                               "sage/typeset/ascii_art.py"
                               "sage/interfaces/gap_workspace.py"
                               "sage/misc/sage_ostools.pyx" ; checks for /bin/sh
                               "sage/repl/ipython_tests.py"

                               ;; downgrade to 5.45 may fix this:
                               ;; https://github.com/sagemath/sage/issues/33718
                               ;; https://sourceforge.net/p/maxima/bugs/3964/
                               "sage/calculus/calculus.py"
                               "sage/interfaces/maxima_lib.py"
                               "sage/functions/exp_integral.py" ; correct, but different form
                               "sage/symbolic/integration/integral.py" ; correct, but exact not floating point
                               "sage/symbolic/relation.py" ; order in minimum different

                               "sage/repl/ipython_kernel/kernel.py" ; deprecation warnings triggered
                                                                    ; by `python-pydevd'

                               ;; TODO
                               "sage/env.py" ; maybe try updating `python-pkgconfig'?
                               "sage/interacts/test_jupyter.rst" ; maybe `python-ipywidgets' is too old?
                               ))))
                        (replace 'check
                          (lambda* (#:key inputs tests? #:allow-other-keys)
                            (when tests?
                              (invoke (search-input-file inputs "/bin/sage")
                                      "-t"
                                      "--nthreads"
                                      (number->string (parallel-job-count))
                                      ;; the file / directory we want to test
                                      "sage"))))
                        (delete 'build)
                        (replace 'install
                          (lambda* (#:key inputs #:allow-other-keys)
                            (let
                                ((target (string-append #$output "/bin"))
                                 (source (search-input-file inputs "/bin/sage")))
                              (mkdir-p target)
                              (symlink source (string-append target "/sage"))))))))
    (inputs (list python-sagemath-standard))
    (native-inputs
     (list python-sagemath-standard
           gcc-toolchain
           gfortran-toolchain))))