summaryrefslogtreecommitdiff
path: root/gnu/packages/algebra.scm
blob: f9ae22b3f392dac4ef1f6c27047c48b0d6279253 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.org>
;;;
;;; 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 algebra)
  #:use-module (gnu packages)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cpp)
  #:use-module (gnu packages documentation)
  #:use-module (gnu packages ed)
  #:use-module (gnu packages flex)
  #:use-module (gnu packages fltk)
  #:use-module (gnu packages gl)
  #:use-module (gnu packages graphviz)
  #:use-module (gnu packages image)
  #:use-module (gnu packages java)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages python)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages shells)
  #:use-module (gnu packages tex)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages xiph)
  #:use-module (gnu packages xorg)
  #:use-module (guix build-system ant)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system cmake)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix utils))


(define-public mpfrcx
  (package
   (name "mpfrcx")
   (version "0.5")
   (source (origin
            (method url-fetch)
            (uri (string-append
                  "http://www.multiprecision.org/downloads/mpfrcx-"
                  version ".tar.gz"))
            (sha256
             (base32
              "1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
   (build-system gnu-build-system)
   (propagated-inputs
     `(("gmp" ,gmp)
       ("mpfr" ,mpfr)
       ("mpc"  ,mpc))) ; Header files are included by mpfrcx.h.
   (synopsis "Arithmetic of polynomials over arbitrary precision numbers")
   (description
    "Mpfrcx is a library for the arithmetic of univariate polynomials over
arbitrary precision real (mpfr) or complex (mpc) numbers, without control
on the rounding.  For the time being, only the few functions needed to
implement the floating point approach to complex multiplication are
implemented.  On the other hand, these comprise asymptotically fast
multiplication routines such as Toom–Cook and the FFT.")
   (license license:lgpl3+)
   (home-page "http://mpfrcx.multiprecision.org/")))

(define-public cm
  (package
   (name "cm")
   (version "0.3")
   (source (origin
            (method url-fetch)
            (uri (string-append
                  "http://www.multiprecision.org/cm/download/cm-"
                  version ".tar.gz"))
            (sha256
             (base32
              "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
   (build-system gnu-build-system)
   (propagated-inputs
     `(("mpfrcx" ,mpfrcx)
       ("zlib" ,zlib))) ; Header files included from cm_common.h.
   (inputs
     `(("pari-gp"  ,pari-gp)))
   (synopsis "CM constructions for elliptic curves")
   (description
    "The CM software implements the construction of ring class fields of
imaginary quadratic number fields and of elliptic curves with complex
multiplication via floating point approximations.  It consists of libraries
that can be called from within a C program and of executable command
line applications.")
   (license license:gpl3+)
   (home-page "http://cm.multiprecision.org/")))

(define-public fplll
  (package
   (name "fplll")
   (version "4.0.4")
   (source (origin
            (method url-fetch)
            (uri (string-append
                  "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
                  version ".tar.gz"))
            (sha256 (base32
                     "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))
   (build-system gnu-build-system)
   (inputs `(("gmp" ,gmp)
             ("mpfr" ,mpfr)))
   (synopsis "Library for LLL-reduction of euclidean lattices")
   (description
    "fplll LLL-reduces euclidean lattices.  Since version 3, it can also
solve the shortest vector problem.")
   (license license:lgpl2.1+)
   (home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/")))

(define-public pari-gp
  (package
    (name "pari-gp")
    (version "2.11.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
                    version ".tar.gz"))
              (sha256
               (base32
                "1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("texlive" ,(texlive-union
                    (list texlive-fonts-amsfonts
                          texlive-latex-amsfonts)))))
    (inputs `(("gmp" ,gmp)
              ("libx11" ,libx11)
              ("perl" ,perl)
              ("readline" ,readline)))
    (arguments
     '(#:make-flags '("all")
       #:test-target "dobench"
       #:phases
       (modify-phases %standard-phases
         (replace 'configure
           (lambda* (#:key outputs #:allow-other-keys)
             (invoke "./Configure"
                     (string-append "--prefix="
                                    (assoc-ref outputs "out"))))))))
    (synopsis "PARI/GP, a computer algebra system for number theory")
    (description
     "PARI/GP is a widely used computer algebra system designed for fast
computations in number theory (factorisations, algebraic number theory,
elliptic curves...), but it also contains a large number of other useful
functions to compute with mathematical entities such as matrices,
polynomials, power series, algebraic numbers, etc., and a lot of
transcendental functions.
PARI is also available as a C library to allow for faster computations.")
    (license license:gpl2+)
    (home-page "https://pari.math.u-bordeaux.fr/")))

(define-public gp2c
  (package
   (name "gp2c")
   (version "0.0.11pl1")
   (source (origin
            (method url-fetch)
            (uri (string-append
                  "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
                  version ".tar.gz"))
            (sha256
              (base32
                "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s"))))
   (build-system gnu-build-system)
   (native-inputs `(("perl" ,perl)))
   (inputs `(("pari-gp" ,pari-gp)))
   (arguments
    '(#:configure-flags
      (list (string-append "--with-paricfg="
                           (assoc-ref %build-inputs "pari-gp")
                           "/lib/pari/pari.cfg"))))
   (synopsis "PARI/GP, a computer algebra system for number theory")
   (description
    "PARI/GP is a widely used computer algebra system designed for fast
computations in number theory (factorisations, algebraic number theory,
elliptic curves...), but it also contains a large number of other useful
functions to compute with mathematical entities such as matrices,
polynomials, power series, algebraic numbers, etc., and a lot of
transcendental functions.
PARI is also available as a C library to allow for faster computations.

GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
   (license license:gpl2)
   (home-page "https://pari.math.u-bordeaux.fr/")))

(define-public cmh
  (package
   (name "cmh")
   (version "1.0")
   (source (origin
            (method url-fetch)
            (uri (string-append
                  "https://gforge.inria.fr/frs/download.php/33497/cmh-"
                  version ".tar.gz"))
            (sha256
             (base32
              "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
   (build-system gnu-build-system)
   (inputs
     `(("gmp" ,gmp)
       ("mpfr" ,mpfr)
       ("mpc" ,mpc)
       ("mpfrcx" ,mpfrcx)
       ("fplll" ,fplll)
       ("pari-gp"  ,pari-gp)))
   (synopsis "Igusa class polynomial computations")
   (description
    "The CMH software computes Igusa (genus 2) class polynomials, which
parameterize the CM points in the moduli space of 2-dimensional abelian
varieties, i.e. Jacobians of hyperelliptic curves.
It can also be used to compute theta constants at arbitrary
precision.")
   (license license:gpl3+)
   (home-page "http://cmh.gforge.inria.fr/")))

(define-public giac-xcas
  (package
    (name "giac-xcas")
    (version "1.5.0-37")
    (source (origin
              (method url-fetch)
              ;; "~parisse/giac" is not used because the maintainer regularly
              ;; overwrites the release tarball there, introducing a checksum
              ;; mismatch every time.  See
              ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
              (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
                                  "~parisse/debian/dists/stable/main/"
                                  "source/giac_" version ".tar.gz"))
              (sha256
               (base32
                "1c6jmswv3ay13n6mjgh9w7nbpdgm5lbwdcmva5sli3vqn4chn3vq"))))
    (build-system gnu-build-system)
    (outputs '("out" "doc"))            ;77MiB of documentation
    (arguments
     `(#:modules ((ice-9 ftw)
                  (guix build utils)
                  (guix build gnu-build-system))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'patch-bin-cp
           ;; Some Makefiles contain hard-coded "/bin/cp".
           (lambda _
             (substitute* (find-files "doc" "^Makefile")
               (("/bin/cp") (which "cp")))
             #t))
         (add-after 'unpack 'disable-failing-test
           ;; FIXME: Test failing.  Not sure why.
           (lambda _
             (substitute* "check/Makefile.in"
               (("chk_fhan11") ""))
             #t))
         (add-after 'install 'install-doc
           ;; Setting --docdir to "doc" output isn't sufficient as
           ;; documentation and examples are scattered throughout the source.
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (doc (assoc-ref outputs "doc"))
                    (docdir (string-append doc
                                           "/share/doc/"
                                           (string-append ,name "-" ,version))))
               ;; For some reason, the install process moves
               ;; "share/giac/examples" instead of "share/giac/doc" to
               ;; "$(docdir)".  Clean up the mess and start over.
               (delete-file-recursively (string-append doc "/share"))
               (mkdir-p docdir)
               (with-directory-excursion out
                 (for-each (lambda (f)
                             (unless (member f '("." ".."))
                               (copy-recursively (string-append "share/giac/" f)
                                                 (string-append docdir "/" f))))
                           (scandir "share/giac"))
                 (delete-file-recursively "share/giac")))
             #t)))))
    (inputs
     `(("fltk" ,fltk)
       ("gmp" ,gmp)
       ("gsl" ,gsl)
       ("lapack" ,lapack)
       ("libao" ,ao)
       ("libjpeg" ,libjpeg)
       ("libpng" ,libpng)
       ("libx11" ,libx11)
       ("libxinerama" ,libxinerama)
       ("libxft" ,libxft)
       ("libxt" ,libxt)
       ("mesa" ,mesa)
       ("mpfi" ,mpfi)
       ("mpfr" ,mpfr)
       ("ntl" ,ntl)
       ("perl" ,perl)
       ("pari-gp" ,pari-gp)
       ("tcsh" ,tcsh)
       ("texlive" ,texlive-tiny)))
    (native-inputs `(("readline" ,readline)))
    (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
    (synopsis "Computer algebra system")
    (description
     "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
maple, mupad and the TI89.  It is available as a standalone program (graphic
or text interfaces) or as a C++ library.")
    (license license:gpl3+)))

(define-public flint
  (package
   (name "flint")
   (version "2.5.2")
   (source (origin
            (method url-fetch)
            (uri (string-append
                  "http://flintlib.org/flint-"
                  version ".tar.gz"))
            (sha256 (base32
                     "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
            (patches (search-patches "flint-ldconfig.patch"))))
   (build-system gnu-build-system)
   (propagated-inputs
    `(("gmp" ,gmp)
      ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
   (arguments
    `(#:parallel-tests? #f ; seems to be necessary on arm
      #:phases
       (modify-phases %standard-phases
         (replace 'configure
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
                   (gmp (assoc-ref inputs "gmp"))
                   (mpfr (assoc-ref inputs "mpfr")))
               ;; do not pass "--enable-fast-install", which makes the
               ;; homebrew configure process fail
               (invoke "./configure"
                       (string-append "--prefix=" out)
                       (string-append "--with-gmp=" gmp)
                       (string-append "--with-mpfr=" mpfr))
               #t))))))
   (synopsis "Fast library for number theory")
   (description
    "FLINT is a C library for number theory.  It supports arithmetic
with numbers, polynomials, power series and matrices over many base
rings, including multiprecision integers and rationals, integers
modulo n, p-adic numbers, finite fields (prime and non-prime order)
and real and complex numbers (via the Arb extension library).

Operations that can be performed include conversions, arithmetic,
GCDs, factoring, solving linear systems, and evaluating special
functions.  In addition, FLINT provides various low-level routines for
fast arithmetic.")
   (license license:gpl2+)
   (home-page "http://flintlib.org/")))

(define-public arb
  (package
    (name "arb")
    (version "2.14.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/fredrik-johansson/arb.git")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1ndxg7h4xvccjgp5l9z2f8b66dsff6fhf86bn5n7f75a1ksd7554"))))
    (build-system gnu-build-system)
    (propagated-inputs
     `(("flint" ,flint)))               ; flint.h is included by arf.h
    (inputs
     `(("gmp" ,gmp)
       ("mpfr" ,mpfr)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'configure
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out"))
                   (flint (assoc-ref inputs "flint"))
                   (gmp (assoc-ref inputs "gmp"))
                   (mpfr (assoc-ref inputs "mpfr")))
               ;; do not pass "--enable-fast-install", which makes the
               ;; homebrew configure process fail
               (invoke "./configure"
                       (string-append "--prefix=" out)
                       (string-append "--with-flint=" flint)
                       (string-append "--with-gmp=" gmp)
                       (string-append "--with-mpfr=" mpfr))))))))
    (synopsis "Arbitrary precision floating-point ball arithmetic")
    (description
     "Arb is a C library for arbitrary-precision floating-point ball
arithmetic.  It supports efficient high-precision computation with
polynomials, power series, matrices and special functions over the
real and complex numbers, with automatic, rigorous error control.")
    (license license:lgpl2.1+)
    (home-page "http://fredrikj.net/arb/")))

(define-public ntl
  (package
   (name "ntl")
   (version "9.7.0")
   (source (origin
            (method url-fetch)
            (uri (string-append "http://shoup.net/ntl/ntl-"
                                version ".tar.gz"))
            (sha256 (base32
                     "115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq"))))
   (build-system gnu-build-system)
   (native-inputs
    `(("libtool" ,libtool)
      ("perl" ,perl))) ; for configuration
   ;; FIXME: Add optional input gf2x once available; then also add
   ;; configure flag "NTL_GF2X_LIB=on".
   (inputs
    `(("gmp" ,gmp)))
   (arguments
    `(#:phases
      (modify-phases %standard-phases
        (replace 'configure
         (lambda* (#:key outputs #:allow-other-keys)
           (chdir "src")
           (system* "./configure"
                    (string-append "PREFIX=" (assoc-ref outputs "out"))
                    ;; Do not build especially for the build machine.
                    "NATIVE=off"
                    ;; Also do not tune to the build machine.
                    "WIZARD=off"
                    "SHARED=on")
           #t)))))
   (synopsis "C++ library for number theory")
   (description
    "NTL is a C++ library providing data structures and algorithms
for manipulating signed, arbitrary length integers, and for vectors,
matrices, and polynomials over the integers and over finite fields.")
   (license license:gpl2+)
   (home-page "http://shoup.net/ntl/")))

(define-public singular
  (package
   (name "singular")
   (version "4.1.1p3")
   (source
    (origin
      (method url-fetch)
      (uri
       (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
                      "Singular/SOURCES/"
                      (string-join
                       (string-split
                        (string-trim-right version #\p
                                           0 (1- (string-length version)))
                        #\.) "-")
                      "/singular-" version ".tar.gz"))
             (sha256 (base32
                      "1qqj9bm9pkzm0iyycpvm8x6s79wws3nq60lz25h8x1q61h3426sm"))))
   (build-system gnu-build-system)
   (native-inputs
    `(("doxygen" ,doxygen)
      ("graphviz" ,graphviz)
      ("perl" ,perl)))
   (inputs
    `(("cddlib" ,cddlib)
      ("gmp" ,gmp)
      ("flint" ,flint)
      ("mpfr" ,mpfr)
      ("ntl" ,ntl)
      ("python" ,python-2)
      ("readline" ,readline)))
   (arguments
    `(#:configure-flags
      (list (string-append "--with-ntl="
                           (assoc-ref %build-inputs "ntl")))))
   (synopsis "Computer algebra system for polynomial computations")
   (description
    "Singular is a computer algebra system for polynomial computations,
with special emphasis on commutative and non-commutative algebra, algebraic
geometry and singularity theory.")
   ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
   ;; libraries with which it links are licensed under lgpl3+, so the
   ;; combined work becomes gpl3. See COPYING in the source code.
   (license license:gpl3)
   (home-page "http://www.singular.uni-kl.de/index.php")))

(define-public gmp-ecm
  (package
   (name "gmp-ecm")
   (version "7.0.4")
   (source (origin
             (method url-fetch)
             ;; Use the ‘Latest version’ link for a stable URI across releases.
             (uri (string-append "https://gforge.inria.fr/frs/download.php/"
                                 "latestfile/160/ecm-" version ".tar.gz"))
             (sha256 (base32
                      "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
   (build-system gnu-build-system)
   (inputs
    `(("gmp" ,gmp)))
   (arguments
    `(#:configure-flags '("--enable-shared"
                          ;; Disable specific assembly routines, which depend
                          ;; on the subarchitecture of the build machine,
                          ;; and use gmp instead.
                          "--disable-asm-redc")))
   (synopsis "Integer factorization library using the elliptic curve method")
   (description
    "GMP-ECM factors integers using the elliptic curve method (ECM) as well
as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
binary.")
   ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
   ;; so the combined work is under gpl3+.
   (license license:gpl3+)
   (home-page "http://ecm.gforge.inria.fr/")))

(define-public bc
  (package
    (name "bc")
    (version "1.07.1")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
             (sha256
              (base32
               "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("ed" ,ed)
       ("flex" ,flex)
       ("texinfo" ,texinfo)))
    (arguments
     '(#:configure-flags
       (list "--with-readline")))
    (home-page "https://www.gnu.org/software/bc/")
    (synopsis "Arbitrary precision numeric processing language")
    (description
     "bc is an arbitrary precision numeric processing language.  It includes
an interactive environment for evaluating mathematical statements.  Its
syntax is similar to that of C, so basic usage is familiar.  It also includes
\"dc\", a reverse-polish calculator.")
    (license license:gpl2+)))

;; The original kiss-fft does not have a complete build system and does not
;; build any shared libraries.  This is a fork used by Extempore.
(define-public kiss-fft-for-extempore
  (package
    (name "kiss-fft-for-extempore")
    (version "1.3.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/extemporelang/kiss_fft.git")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
    (build-system cmake-build-system)
    (arguments `(#:tests? #f)) ; no tests included
    ;; Extempore refuses to build on architectures other than x86_64
    (supported-systems '("x86_64-linux"))
    (home-page "https://github.com/extemporelang/kiss_fft")
    (synopsis "Mixed-radix Fast Fourier Transform")
    (description
     "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
that can use fixed or floating data types and can easily be incorporated into
a C program.")
    (license license:bsd-3)))

(define-public fftw
  (package
    (name "fftw")
    (version "3.3.8")
    (source (origin
             (method url-fetch)
             (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
                                 version".tar.gz"))
             (sha256
              (base32
               "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
    (build-system gnu-build-system)
    (arguments
     `(#:configure-flags
       '("--enable-shared" "--enable-openmp" "--enable-threads"
         ,@(let ((system (or (%current-target-system) (%current-system))))
             ;; Enable SIMD extensions for codelets.  See details at:
             ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
             (cond
              ((string-prefix? "x86_64" system)
               '("--enable-sse2" "--enable-avx" "--enable-avx2"
                 "--enable-avx512" "--enable-avx-128-fma"))
              ((string-prefix? "i686" system)
               '("--enable-sse2"))
              ((string-prefix? "aarch64" system)
               ;; Note that fftw supports NEON on 32-bit ARM only when
               ;; compiled for single-precision.
               '("--enable-neon"))
              (else
               '())))
         ;; By default '-mtune=native' is used.  However, that may cause the
         ;; use of ISA extensions (e.g. AVX) that are not necessarily
         ;; available on the user's machine when that package is built on a
         ;; different machine.
         "ax_cv_c_flags__mtune_native=no")))
    (native-inputs `(("perl" ,perl)))
    (home-page "http://fftw.org")
    (synopsis "Computing the discrete Fourier transform")
    (description
     "FFTW is a C subroutine library for computing the discrete Fourier
transform (DFT) in one or more dimensions, of arbitrary input size, and of
both real and complex data (as well as of even/odd data---i.e. the discrete
cosine/ sine transforms or DCT/DST).")
    (license license:gpl2+)))

(define-public fftwf
  (package (inherit fftw)
    (name "fftwf")
    (arguments
     (substitute-keyword-arguments (package-arguments fftw)
       ((#:configure-flags fftw-configure-flags)
        `(cons* "--enable-single"
                ,@(if (string-prefix? "arm" (or (%current-target-system)
                                                (%current-system)))
                      ;; fftw supports NEON on 32-bit ARM only when compiled
                      ;; for single-precision, so add it here.
                      '("--enable-neon")
                      '())
                ,fftw-configure-flags))))
    (description
     (string-append (package-description fftw)
                    "  Single-precision version."))))

(define-public fftw-openmpi
  (package (inherit fftw)
    (name "fftw-openmpi")
    (inputs
     `(("openmpi" ,openmpi)
       ,@(package-inputs fftw)))
    (arguments
     (substitute-keyword-arguments (package-arguments fftw)
       ((#:configure-flags cf)
        `(cons "--enable-mpi" ,cf))
       ((#:phases phases '%standard-phases)
        `(modify-phases ,phases
           (add-before 'check 'mpi-setup
             ,%openmpi-setup)))))
    (description
     (string-append (package-description fftw)
                    "  With OpenMPI parallelism support."))))

(define-public java-la4j
  (package
    (name "java-la4j")
    (version "0.6.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/vkostyukov/la4j.git")
                    (commit version)))
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
                "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
    (build-system ant-build-system)
    (arguments
     `(#:jar-name "la4j.jar"
       #:jdk ,icedtea-8
       #:test-exclude (list "**/Abstract*.java"
                            "**/MatrixTest.java"
                            "**/DenseMatrixTest.java"
                            "**/SparseMatrixTest.java"
                            "**/VectorTest.java"
                            "**/SparseVectorTest.java"
                            "**/DenseVectorTest.java")))
    (native-inputs
     `(("java-junit" ,java-junit)
       ("java-hamcrest-core" ,java-hamcrest-core)))
    (home-page "http://la4j.org/")
    (synopsis "Java library that provides Linear Algebra primitives and algorithms")
    (description "The la4j library is a Java library that provides Linear
Algebra primitives (matrices and vectors) and algorithms.  The key features of
the la4j library are:

@itemize
@item No dependencies and tiny size
@item Fluent object-oriented/functional API
@item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
@item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
@item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
@item MatrixMarket/CSV IO formats support for matrices and vectors
@end itemize\n")
    (license license:asl2.0)))

(define-public java-jlargearrays
  (package
    (name "java-jlargearrays")
    (version "1.6")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://search.maven.org/remotecontent?"
                                  "filepath=pl/edu/icm/JLargeArrays/"
                                  version "/JLargeArrays-" version
                                  "-sources.jar"))
              (file-name (string-append name "-" version ".jar"))
              (sha256
               (base32
                "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
    (build-system ant-build-system)
    (arguments
     `(#:jar-name "jlargearrays.jar"
       #:tests? #f ; tests are not included in the release archive
       #:jdk ,icedtea-8))
    (propagated-inputs
     `(("java-commons-math3" ,java-commons-math3)))
    (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
    (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
    (description "JLargeArrays is a Java library of one-dimensional arrays
that can store up to 263 elements.")
    (license license:bsd-2)))

(define-public java-jtransforms
  (package
    (name "java-jtransforms")
    (version "3.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://search.maven.org/remotecontent?"
                                  "filepath=com/github/wendykierp/JTransforms/"
                                  version "/JTransforms-" version "-sources.jar"))
              (sha256
               (base32
                "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
    (build-system ant-build-system)
    (arguments
     `(#:jar-name "jtransforms.jar"
       #:tests? #f ; tests are not included in the release archive
       #:jdk ,icedtea-8))
    (propagated-inputs
     `(("java-commons-math3" ,java-commons-math3)
       ("java-jlargearrays" ,java-jlargearrays)))
    (home-page "https://github.com/wendykierp/JTransforms")
    (synopsis "Multithreaded FFT library written in pure Java")
    (description "JTransforms is a multithreaded FFT library written in pure
Java.  Currently, four types of transforms are available: @dfn{Discrete
Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
    (license license:bsd-2)))

(define-public eigen
  (package
    (name "eigen")
    (version "3.3.5")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
                                  version ".tar.bz2"))
              (sha256
               (base32
                "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk"))
              (file-name (string-append name "-" version ".tar.bz2"))
              (modules '((guix build utils)))
              (snippet
               ;; There are 3 test failures in the "unsupported" directory,
               ;; but maintainers say it's a known issue and it's unsupported
               ;; anyway, so just skip them.
               '(begin
                  (substitute* "unsupported/CMakeLists.txt"
                    (("add_subdirectory\\(test.*")
                     "# Do not build the tests for unsupported features.\n"))
                  #t))))
    (build-system cmake-build-system)
    (arguments
     '(;; Turn off debugging symbols to save space.
       #:build-type "Release"

       #:phases (modify-phases %standard-phases
                  (replace 'check
                    (lambda _
                      (let* ((cores  (parallel-job-count))
                             (dash-j (format #f "-j~a" cores)))
			(setenv "EIGEN_SEED" "1") ;for reproducibility
                        ;; First build the tests, in parallel.  See
                        ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
                        (invoke "make" "buildtests" dash-j)

                        ;; Then run 'CTest' with -V so we get more
                        ;; details upon failure.
                        (invoke "ctest" "-V" dash-j)))))))
    (home-page "https://eigen.tuxfamily.org")
    (synopsis "C++ template library for linear algebra")
    (description
     "Eigen is a C++ template library for linear algebra: matrices, vectors,
numerical solvers, and related algorithms.  It provides an elegant API based
on \"expression templates\".  It is versatile: it supports all matrix sizes,
all standard numeric types, various matrix decompositions and geometry
features, and more.")

    ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
    ;; See 'COPYING.README' for details.
    (license license:mpl2.0)))

(define-public xtensor
  (package
    (name "xtensor")
    (version "0.17.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/QuantStack/xtensor.git")
                    (commit version)))
              (sha256
               (base32
                "0w40v5lp0hp8ihf8nnvak373sb5xx0768pxgiqh3nzn57wf8px4r"))
              (file-name (git-file-name name version))))
    (build-system cmake-build-system)
    (native-inputs
     `(("googletest" ,googletest)
       ("xtl" ,xtl)))
    (arguments
     `(#:configure-flags
       '("-DBUILD_TESTS=ON")
       #:test-target "xtest"))
    (home-page "http://quantstack.net/xtensor")
    (synopsis "C++ tensors with broadcasting and lazy computing")
    (description "xtensor is a C++ library meant for numerical analysis with
multi-dimensional array expressions.

xtensor provides:
@itemize
@item an extensible expression system enabling lazy broadcasting.
@item an API following the idioms of the C++ standard library.
@item tools to manipulate array expressions and build upon xtensor.
@end itemize")
    (license license:bsd-3)))

(define-public gap
  (package
    (name "gap")
    (version "4.10.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
                           (version-major+minor version)
                           "/tar.bz2/gap-"
                           version
                           ".tar.bz2"))
       (sha256
        (base32
         "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird"))
       (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
       (snippet
        '(begin
           ;; Delete the external gmp and zlib libraries
           ;; and a subdirectory not needed for our build.
           (for-each delete-file-recursively
                     '("extern" "hpcgap"))
           ;; Delete a failing test.
           ;; FIXME: This might be fixed in the next release, see
           ;; https://github.com/gap-system/gap/issues/3292
           (delete-file "tst/testinstall/dir.tst")
           ;; Delete all packages except for a fixed list.
           (with-directory-excursion "pkg"
             (for-each delete-file-recursively
               (lset-difference string=? (scandir ".")
                 '("." ".."
                   ;; Necessary packages.
                   "GAPDoc-1.6.2"
                   "primgrp-3.3.2"
                   "SmallGrp-1.3"    ; artistic2.0
                   "transgrp"        ; artistic2.0 for data,
                                     ; gpl2 or gpl3 for code
                   ;; Recommanded package.
                   "io-4.5.4"        ; gpl3+
                   ;; Optional packages, searched for at start,
                   ;; and their depedencies.
                   "alnuth-3.1.0"
                   "AutoDoc-2018.09.20"
                   "autpgrp-1.10"
                   "crisp-1.4.4"     ; bsd-2
                   ; "ctbllib"       ; no explicit license, drop
                   "FactInt-1.6.2"
                   "fga"
                   "irredsol-1.4"    ; bsd-2
                   "laguna-3.9.0"
                   "polenta-1.3.8"
                   "polycyclic-2.14"
                   "radiroot-2.8"
                   "resclasses-4.7.1"
                   "sophus-1.24"
                   ; "tomlib-1.2.7"  ; no explicit license, drop
                   "utils-0.59"))))
           #t))))
    (build-system gnu-build-system)
    (inputs
     `(("gmp" ,gmp)
       ("zlib" ,zlib)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'build 'build-packages
           ;; Compile all packages that have not been deleted by the
           ;; code snippet above.
           (lambda _
             (setenv "CONFIG_SHELL" (which "bash"))
             (with-directory-excursion "pkg"
               (invoke "../bin/BuildPackages.sh")
             #t)))
         (add-after 'build-packages 'build-doc
           ;; The documentation is bundled, but we create it from source.
           (lambda _
             (with-directory-excursion "doc"
               (invoke "./make_doc"))
             #t))
         (replace 'check
           (lambda _
             ;; "make check" is expected to appear in gap-4.10.1
             (invoke "./gap" "tst/testinstall.g")
             #t))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (prog (string-append bin "/gap"))
                    (prog-real (string-append bin "/.gap-real"))
                    (share (string-append out "/share/gap"))
                    (include (string-append out "/include/gap")))
               ;; Install only the gap binary; the gac compiler is left
               ;; for maybe later. "Wrap" it in a shell script that calls
               ;; the binary with the correct parameter.
               (mkdir-p bin)
               (copy-file "gap" prog-real)
               (call-with-output-file prog
                 (lambda (port)
                   (format port
                           "#!~a~%exec ~a -l ~a \"$@\"~%"
                           (which "bash")
                           prog-real
                           share)))
               (chmod prog #o755)
               ;; Install the headers and the library, which are needed by
               ;; Sage. The Makefile targets are available in gap-4.10.0,
               ;; but planned to be removed in gap-4.10.1.
               (invoke "make" "install-headers")
               (invoke "make" "install-libgap")
               (install-file "gen/config.h" include)
               ;; Install a certain number of files and directories to
               ;; SHARE, where the wrapped shell script expects them.
               ;; Remove information on the build directory from sysinfo.gap.
               (substitute* "sysinfo.gap"
                 (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
                 (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
                 (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
               (install-file "sysinfo.gap" share)
               (copy-recursively "grp" (string-append share "/grp"))
               (copy-recursively "pkg" (string-append share "/pkg"))
               ;; The following is not the C library libgap.so, but a
               ;; library of GAP code.
               (copy-recursively "lib" (string-append share "/lib"))
               ;; The gap binary looks for documentation inside SHARE.
               (copy-recursively "doc" (string-append share "/doc")))
             #t)))))
    (home-page "https://www.gap-system.org/")
    (synopsis
     "System for computational group theory")
    (description
     "GAP is a system for computational discrete algebra, with particular
emphasis on computational group theory.  It provides a programming language,
a library of thousands of functions implementing algebraic algorithms
written in the GAP language as well as large data libraries of algebraic
objects.")
    ;; Some packages have different licenses (effectively forcing the
    ;; combined work to be licensed as gpl3+); if this is the case, this
    ;; is mentioned above next to their name.
    ;; Some packages have no license mentioned explicitly; supposedly this
    ;; means that the gpl2+ licence of GAP itself applies, but to be on the
    ;; safe side, we drop them for now.
    (license license:gpl2+)))