unofficial mirror of guix-patches@gnu.org 
 help / color / mirror / code / Atom feed
blob af50c2d7758988ec6ad55536e839e287dc8ba609 63593 bytes (raw)
name: gnu/packages/algebra.scm 	 # note: path name is non-authoritative(*)

   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
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
 
;;; 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, 2020 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, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;;
;;; 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 bison)
  #: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 pkg-config)
  #:use-module (gnu packages pulseaudio)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz)
  #: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 build-system python)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix hg-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://www.multiprecision.org/mpfrcx/")))

(define-public gf2x
  (package
   (name "gf2x")
   (version "1.2")
   (source (origin
            (method url-fetch)
            (uri (string-append
                  "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
                  version ".tar.gz"))
            (sha256
             (base32
              "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
   (build-system gnu-build-system)
   (synopsis "Arithmetic of polynomials over binary finite fields")
   (description
    "The gf2x library provides arithmetic of polynomials over finite fields
of characteristic 2.  It implements the multiplication, squaring and
greatest common divisor operations.")
   (license license:gpl3+)
   (home-page "https://gforge.inria.fr/projects/gf2x/")))

(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://www.multiprecision.org/cm/")))

(define-public fplll
  (package
    (name "fplll")
    (version "5.2.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/fplll/fplll.git")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (inputs
     `(("gmp" ,gmp)
       ("mpfr" ,mpfr)))
    (home-page "https://github.com/fplll/fplll")
    (synopsis "Library for LLL-reduction of euclidean lattices")
    (description
     "fplll contains implementations of several lattice algorithms.
The implementation relies on floating-point orthogonalization, and LLL
is central to the code, hence the name.

It includes implementations of floating-point LLL reduction
algorithms, offering different speed/guarantees ratios.  It contains
a @emph{wrapper} choosing the estimated best sequence of variants in
order to provide a guaranteed output as fast as possible.  In the case
of the wrapper, the succession of variants is oblivious to the user.

It includes an implementation of the BKZ reduction algorithm,
including the BKZ-2.0 improvements (extreme enumeration
pruning, pre-processing of blocks, early termination).  Additionally,
Slide reduction and self dual BKZ are supported.

It also includes a floating-point implementation of the
Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
vector.  For the same task, the GaussSieve algorithm is also available
in fplll.  Finally, it contains a variant of the enumeration algorithm
that computes a lattice vector closest to a given vector belonging to
the real span of the lattice.")
    (license license:lgpl2.1+)))

(define-public python-fpylll
  (package
    (name "python-fpylll")
    (version "0.4.1")
    (source
     (origin
       ;; Pypi contains and older release, so we use a tagged release from
       ;; Github instead.
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/fplll/fpylll.git")
             (commit (string-append version "dev"))))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
    (build-system python-build-system)
    (inputs
     `(("fplll" ,fplll)
       ("gmp" ,gmp)
       ("mpfr" ,mpfr)
       ("pari-gp" ,pari-gp)))
    (propagated-inputs
     `(("cysignals" ,python-cysignals)
       ("cython" ,python-cython)
       ("flake8" ,python-flake8)
       ("numpy" ,python-numpy)
       ("pytest" ,python-pytest)))
    (home-page "https://github.com/fplll/fpylll")
    (synopsis "Python interface for fplll")
    (description "fpylll is a Python wrapper for fplll.")
    (license license:gpl2+)))

(define-public pari-gp
  (package
    (name "pari-gp")
    (version "2.11.2")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
                    version ".tar.gz"))
              (sha256
               (base32
                "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("texlive" ,(texlive-union
                    (list texlive-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 "0.0.11pl2")
   (source (origin
            (method url-fetch)
            (uri (string-append
                  "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
                  version ".tar.gz"))
            (sha256
              (base32
                "0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g"))))
   (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 fplll-4-cmh
  (package
    (inherit fplll)
    (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"))))))

(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-4-cmh)
       ("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
  (package
    (name "giac")
    (version "1.5.0-87")
    (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 "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv"))))
    (build-system gnu-build-system)
    (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 'fix-doc
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               ;; Most French documentation has a non-commercial
               ;; license, so we need to remove it.
               (with-directory-excursion (string-append out "/share/giac/doc/fr")
                 (for-each delete-file-recursively
                           '("cascas" "casexo" "casgeo" "casrouge" "cassim"
                             "castor")))
               ;; Remove duplicate documentation in
               ;; "%out/share/doc/giac/", where Xcas does not expect
               ;; to find it.
               (delete-file-recursively (string-append out "/share/doc/giac"))
               #t)))
         (add-after 'install 'remove-unnecessary-executable
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               (delete-file (string-append out "/bin/xcasnew"))
               #t))))))
    (inputs
     ;;; TODO: Add libnauty.
     `(("fltk" ,fltk)
       ("glpk" ,glpk)
       ("gmp" ,gmp)
       ("gsl" ,gsl)
       ("lapack" ,lapack)
       ("libao" ,ao)
       ("libjpeg" ,libjpeg)
       ("libpng" ,libpng)
       ("libsamplerate" ,libsamplerate)
       ("libx11" ,libx11)
       ("libxinerama" ,libxinerama)
       ("libxft" ,libxft)
       ("libxt" ,libxt)
       ("mesa" ,mesa)
       ("mpfi" ,mpfi)
       ("mpfr" ,mpfr)
       ("ntl" ,ntl)
       ("perl" ,perl)
       ("pari-gp" ,pari-gp)
       ("tcsh" ,tcsh)))
    (native-inputs
     `(("bison" ,bison)
       ("flex" ,flex)
       ("readline" ,readline)
       ("texlive" ,texlive-tiny)))
    (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 "2.17.0")
    (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
                "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
    (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://arblib.org")))

(define-public python-flint
  (package
    (name "python-flint")
    (version "0.3.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/fredrik-johansson/python-flint.git")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
              (patches (search-patches "python-flint-includes.patch"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-cython" ,python-cython)))
    (propagated-inputs
     `(("python-numpy" ,python-numpy)))
    (inputs
     `(("arb" ,arb)
       ("flint" ,flint)))
    (synopsis "Python module wrapping ARB and FLINT")
    (description
     "Python-flint is a Python extension module wrapping FLINT
(Fast Library for Number Theory) and Arb (arbitrary-precision ball
arithmetic).  It supports integers, rationals, modular integers,
real and complex ball arithmetic, polynomials and matrices over all
these types and other mathematical functions.")
    (license license:expat)
    (home-page "http://fredrikj.net/python-flint/")))

(define-public ntl
  (package
   (name "ntl")
   (version "11.4.3")
   (source (origin
            (method url-fetch)
            (uri (string-append "https://shoup.net/ntl/ntl-"
                                version ".tar.gz"))
            (sha256
             (base32
              "1lisp3064rch3jaa2wrhy1s9kll7i3ka3d0y6lj6l3l4ckfcrhdp"))
            (modules '((guix build utils)))
            (snippet
             '(begin
                (delete-file-recursively "src/libtool-origin")
                #t))))
   (build-system gnu-build-system)
   (native-inputs
    `(("libtool" ,libtool)
      ("perl" ,perl))) ; for configuration
   (inputs
    `(("gmp" ,gmp)
      ("gf2x" ,gf2x)))
   (arguments
    `(#:phases
      (modify-phases %standard-phases
        (replace 'configure
         (lambda* (#:key inputs outputs #:allow-other-keys)
           (chdir "src")
           (invoke "./configure"
                    (string-append "PREFIX=" (assoc-ref outputs "out"))
                    (string-append "LIBTOOL=" (assoc-ref inputs "libtool") "/bin/libtool")
                    ;; set the library prefixes explicitly so that they get
                    ;; embedded in the .la file
                    (string-append "GMP_PREFIX=" (assoc-ref inputs "gmp"))
                    (string-append "GF2X_PREFIX=" (assoc-ref inputs "gf2x"))
                    ;; Do not build especially for the build machine.
                    "NATIVE=off"
                    "NTL_GF2X_LIB=on"
                    "SHARED=on"))))))
   (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 "https://shoup.net/ntl/")))

(define-public singular
  (package
   (name "singular")
   (version "4.1.2p1")
   (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
                      "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
   (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 "https://repo1.maven.org/maven2/"
                                  "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 "https://repo1.maven.org/maven2/"
                                  "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 "3.3.7")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
                                  version ".tar.bz2"))
              (sha256
               (base32
                "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
              (file-name (string-append name "-" version ".tar.bz2"))
              (patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
              (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 eigen-for-tensorflow
  (let ((changeset "fd6845384b86")
        (revision "1"))
    (package (inherit eigen)
      (name "eigen-for-tensorflow")
      (version (string-append "3.3.5-" revision "." changeset))
      (source (origin
                (method hg-fetch)
                (uri (hg-reference
                      (url "https://bitbucket.org/eigen/eigen")
                      (changeset changeset)))
                (sha256
                 (base32
                  "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
                (file-name (string-append name "-" version "-checkout"))
                (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)))))))

(define-public xtensor
  (package
    (name "xtensor")
    (version "0.20.10")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/QuantStack/xtensor.git")
                    (commit version)))
              (sha256
               (base32
                "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
              (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 "https://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 "4.10.2")
    (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 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
       (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"
                   "autpgrp-1.10"
                   "crisp-1.4.4"     ; bsd-2
                   "ctbllib"       ; gpl3+ according to doc/chap0.txt
                   "FactInt-1.6.2"
                   "fga"
                   "irredsol-1.4"    ; bsd-2
                   "laguna-3.9.2"
                   "polenta-1.3.8"
                   "polycyclic-2.14"
                   "radiroot-2.8"
                   "resclasses-4.7.1"
                   "sophus-1.24"
                   "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
                                   ; and the next release
                   "utils-0.59"))))
           #t))))
    (build-system gnu-build-system)
    (inputs
     `(("gmp" ,gmp)
       ("zlib" ,zlib)))
    (arguments
     `(#:modules ((ice-9 ftw)
                  (srfi srfi-26)
                  (guix build gnu-build-system)
                  (guix build utils))
       #: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 'install
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (lib (string-append out "/lib"))
                    (prog (string-append bin "/gap"))
                    (prog-real (string-append bin "/.gap-real"))
                    (share (string-append out "/share/gap"))
                    (include (string-append out "/include/gap"))
                    (include-hpc (string-append include "/hpc")))
               ;; 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 \"$@\"~%"
                           (which "bash")
                           prog-real
                           share)))
               (chmod prog #o755)
               ;; Install the headers, which are needed by Sage. The
               ;; Makefile target "install-headers" was available in
               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
               (mkdir-p include-hpc)
               (install-file "gen/config.h" include)
               (let ((file-name-predicate-without-stat
                       (lambda (regex)
                         (cut (file-name-predicate regex) <> #f))))
                 (with-directory-excursion "src"
                   (for-each
                     (cut install-file <> include)
                     (scandir "."
                              (file-name-predicate-without-stat ".*\\.h$"))))
                 (with-directory-excursion "src/hpc"
                   (for-each
                     (cut install-file <> include-hpc)
                     (scandir "."
                              (file-name-predicate-without-stat ".*\\.h$")))))
               ;; Install the library, which is needed by Sage. The
               ;; Makefile target "install-libgap" was available in
               ;; gap-4.10.0, but has been commented out in gap-4.10.1.
               ;; Compared to the Makefile, which used libtool, the
               ;; following approach of copying files and making symlinks
               ;; is rather pedestrian. There is hope that some later
               ;; version of gap reinstates and completes the install
               ;; targets.
               (invoke "make" "libgap.la")
               (install-file "libgap.la" lib)
               (install-file ".libs/libgap.so.0.0.0" lib)
               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so")) 
               (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
               ;; 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+)))

(define-public givaro
  (package
    (name "givaro")
    (version "4.1.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/linbox-team/givaro")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (propagated-inputs
     `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'bootstrap 'setenv
           ;; Prevent the autogen.sh script to carry out the configure
           ;; script, which has not yet been patched to replace /bin/sh.
           (lambda _
             (setenv "NOCONFIGURE" "yes")
             #t)))))
    (synopsis "Algebraic computations with exact rings and fields")
    (description
     "Givaro is a C++ library implementing the basic arithmetic of various
algebraic objects: prime fields, extension fields, finite fields, finite
rings, polynomials, algebraic numbers, arbitrary precision integers and
rationals (C++ wrappers over gmp), fixed precision integers.  It also
provides data-structures and templated classes for the manipulation of
compound objects, such as vectors, matrices and univariate polynomials.")
    (license license:cecill-b)
    (home-page "https://github.com/linbox-team/givaro")))

(define-public fflas-ffpack
  (package
    (name "fflas-ffpack")
    (version "2.4.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/linbox-team/fflas-ffpack")
                    (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("openblas" ,openblas)))
    (propagated-inputs
     `(("givaro" ,givaro))) ; required according to the .pc file
    (arguments
     `(#:configure-flags
       (list (string-append "--with-blas-libs="
                            (assoc-ref %build-inputs "openblas")
                            "/lib/libopenblas.so"))
       #:phases
       (modify-phases %standard-phases
         (add-before 'bootstrap 'setenv
           ;; Prevent the autogen.sh script to carry out the configure
           ;; script, which has not yet been patched to replace /bin/sh.
           (lambda _
             (setenv "NOCONFIGURE" "yes")
             #t)))))
    (synopsis "C++ library for linear algebra over finite fields")
    (description
     "FFLAS-FFPACK is a C++ template library for basic linear algebra
operations over a finite field.
FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
of a subset of routines of the numerical BLAS; it also supports sparse
matrix-vector products.
FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
library to provide functionalities of higher level, using the kernel
of a BLAS.  Additionally, it provides routines specific to exact linear
algebra, such as the row echelon form.")
    (license license:lgpl2.1+)
    (home-page "https://linbox-team.github.io/fflas-ffpack/")))

(define-public linbox
  (package
    (name "linbox")
    (version "1.6.3")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/linbox-team/linbox")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("fflas-ffpack" ,fflas-ffpack)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'bootstrap 'setenv
           ;; Prevent the autogen.sh script to carry out the configure
           ;; script, which has not yet been patched to replace /bin/sh.
           (lambda _
             (setenv "NOCONFIGURE" "yes")
             #t)))))
    (synopsis "C++ library for linear algebra over exact rings")
    (description
     "LinBox is a C++ template library for exact linear algebra computation
with dense, sparse, and structured matrices over the integers and over
finite fields.")
    (license license:lgpl2.1+)
    (home-page "https://linbox-team.github.io/linbox/")))

(define-public m4ri
  (package
    (name "m4ri")
    (version "20140914")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://bitbucket.org/malb/m4ri")
                    (commit (string-append "release-" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("libpng" ,libpng)))
    (synopsis "Arithmetic of dense matrices over F_2")
    (description "M4RI is a library for fast arithmetic with dense matrices
over F2.  The name M4RI comes from the first implemented algorithm: The
Method of the Four Russians inversion algorithm published by Gregory Bard.
This algorithm in turn is named after the Method of the Four Russians
multiplication algorithm.")
    (license license:gpl2+)
    (home-page "https://bitbucket.org/malb/m4ri/")))

(define-public symmetrica
  (package
    (name "symmetrica")
    (version "2.0")
    (source (origin
              (method url-fetch/tarbomb)
              (uri (let ((v (string-join (string-split version #\.) "_")))
                     (string-append "http://www.algorithm.uni-bayreuth.de/"
                                    "en/research/SYMMETRICA/"
                                    "SYM" v "_tar.gz")))
              (sha256
               (base32
                "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
              ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
              (patches (search-patches "symmetrica-bruch.patch"
                                       "symmetrica-int32.patch"
                                       "symmetrica-return_values.patch"
                                       "symmetrica-sort_sum_rename.patch"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f                      ;no test
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-makefile
           (lambda _
             (substitute* "makefile"
               (("cc -c") "gcc -c -fPIC"))
             #t))
         (add-after 'fix-makefile 'turn-off-banner
           (lambda _
             (substitute* "de.c"
               (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
             #t))
         (delete 'configure)            ;no configure script
         (replace 'install              ;no install target
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (lib (string-append out "/lib"))
                    (inc (string-append out "/include/symmetrica"))
                    (doc (string-append out "/share/doc/symmetrica-" ,version))
                    (static "libsymmetrica.a"))
               ;; Build static library.
               (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
               (invoke "ranlib" static)
               ;; Install static library and headers.
               (for-each (lambda (f) (install-file f inc))
                         (find-files "." "\\.h$"))
               (install-file "libsymmetrica.a" lib)
               ;; Install documentation.
               (for-each (lambda (f) (install-file f doc))
                         (find-files "." "\\.doc$"))
               #t))))))
    (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
    (synopsis "Combinatoric C Library")
    (description "Symmetrica is a library for combinatorics.  It has support
for the representation theory of the symmetric group and related groups,
combinatorics of tableaux, symmetric functions and polynomials, Schubert
polynomials, and the representation theory of Hecke algebras of type A_n.")
    (license license:public-domain)))

(define-public m4rie
  (package
    (name "m4rie")
    (version "20150908")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://bitbucket.org/malb/m4rie")
                    (commit (string-append "release-" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (inputs
     `(("m4ri" ,m4ri)))
    (synopsis "Arithmetic of dense matrices over F_{2^e}")
    (description "M4RI is a library for fast arithmetic with dense matrices
over finite fields of characteristic 2.  So it extends the functionality
of M4RI from F_2 to F_{2^e}.")
    (license license:gpl2+)
    (home-page "https://bitbucket.org/malb/m4rie/")))

(define-public eclib
  (package
    (name "eclib")
    (version "20190909")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/JohnCremona/eclib/")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (inputs
     `(("ntl" ,ntl)
       ("pari-gp" ,pari-gp)))
    (synopsis "Ranks of elliptic curves and modular symbols")
    (description "The eclib package includes mwrank (for 2-descent on
elliptic curves over Q) and modular symbol code; it has been written by
John Cremona to compute his elliptic curve database.")
    (license license:gpl2+)
    (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
                              "J.E.Cremona/mwrank/index.html"))))

(define-public lrcalc
  (package
    (name "lrcalc")
    (version "1.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://bitbucket.org/asbuch/lrcalc")
                    (commit (string-append "lrcalc-" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
              (patches (search-patches "lrcalc-includes.patch"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'build 'fix-permission
           (lambda _
             (chmod "lrcalc.maple.src" #o644)
             #t)))))
    (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
    (description "The Littlewood-Richardson Calculator (lrcalc) is a
program designed to compute Littlewood-Richardson coefficients.  It computes
single Littlewood-Richardson coefficients, products of Schur functions, or
skew Schur functions.  In addition it computes products in the small quantum
cohomology ring of a Grassmann variety.  The software package also includes
a program that performs fast computation of the more general multiplicative
structure constants of Schubert polynomials.")
    (license license:gpl2+)
    (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))

(define-public iml
  (package
    (name "iml")
    (version "1.0.5")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
                           version ".tar.bz2"))
       (sha256
        (base32
         "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
    (build-system gnu-build-system)
    (inputs
     `(("gmp", gmp)
       ("cblas" ,openblas))) ; or any other BLAS library; the documentation
                             ; mentions ATLAS in particular
    (arguments
     `(#:configure-flags
       (list
        "--enable-shared"
        (string-append "--with-gmp-include="
                       (assoc-ref %build-inputs "gmp") "/include")
        (string-append "--with-gmp-lib="
                       (assoc-ref %build-inputs "gmp") "/lib")
        "--with-cblas=-lopenblas"
        (string-append "--with-cblas-include="
                       (assoc-ref %build-inputs "cblas") "/include")
        (string-append "--with-cblas-lib="
                       (assoc-ref %build-inputs "cblas") "/lib"))))
    (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
    (synopsis
     "Solver for systems of linear equations over the integers")
    (description
     "IML is a C library implementing algorithms for computing exact
solutions to dense systems of linear equations over the integers.
Currently, IML provides the following functionality:

@itemize
@item Nonsingular rational system solving:
compute the unique rational solution X to the system AX=B, where A and B
are integer matrices, A nonsingular.
@item Compute the right nullspace or kernel of an integer matrix.
@item Certified linear system solving:
compute a minimal denominator solution x to a system Ax=b, where b is an
integer vector and A is an integer matrix with arbitrary shape and
rank profile.
@end itemize

In addition, IML provides some low level routines for a variety of mod p
matrix operations: computing the row-echelon form, determinant, rank
profile, and inverse of a mod p matrix. These mod p routines are not
general purpose; they require that p satisfy some preconditions based on
the dimension of the input matrix (usually p should be prime and should be
no more than about 20 bits long).")
    (license license:bsd-3)))

debug log:

solving af50c2d775 ...
found af50c2d775 in https://git.savannah.gnu.org/cgit/guix.git

(*) Git path names are given by the tree(s) the blob belongs to.
    Blobs themselves have no identifier aside from the hash of its contents.^

Code repositories for project(s) associated with this public inbox

	https://git.savannah.gnu.org/cgit/guix.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).