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
|
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2016, 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
;;; Copyright © 2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2022 Malte Frank Gerdes <malte.f.gerdes@gmail.com>
;;; Copyright © 2022 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2022 Paul A. Patience <paul@apatience.com>
;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz>
;;;
;;; 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 python-science)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages cpp)
#:use-module (gnu packages databases)
#:use-module (gnu packages gcc)
#:use-module (gnu packages image-processing)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages simulation)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages statistics)
#:use-module (gnu packages time)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (guix packages)
#:use-module (guix gexp)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (guix build-system python))
(define-public python-scipy
(package
(name "python-scipy")
(version "1.8.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scipy" version))
(sha256
(base32 "1gghkwn93niyasm36333xbqrnn3yiadq9d97wnc9mg14nzbg5m1i"))))
(outputs '("out" "doc"))
(build-system python-build-system)
(arguments
(list
#:modules '((guix build utils)
(guix build python-build-system)
(ice-9 format))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'disable-pythran
(lambda _
(setenv "SCIPY_USE_PYTHRAN" "0")))
(add-before 'build 'change-home-dir
(lambda _
;; Change from /homeless-shelter to /tmp for write permission.
(setenv "HOME" "/tmp")))
(add-before 'build 'configure-openblas
(lambda _
(call-with-output-file "site.cfg"
(lambda (port)
(format port
"\
[blas]
libraries = openblas
library_dirs = ~a/lib
include_dirs = ~:*~a/include
[atlas]
library_dirs = ~:*~a/lib
atlas_libs = openblas~%" #$(this-package-input "openblas"))))))
(add-before 'build 'parallelize-build
(lambda _
(setenv "NPY_NUM_BUILD_JOBS"
(number->string (parallel-job-count)))))
(add-before 'check 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
(doc (string-append data "/doc/" #$name "-" #$version))
(html (string-append doc "/html")))
(with-directory-excursion "doc"
;; Build doc.
(invoke "make" "html"
;; Building the documentation takes a very long time.
;; Parallelize it.
(string-append "SPHINXOPTS=-j"
(number->string (parallel-job-count))))
;; Install doc.
(mkdir-p html)
(copy-recursively "build/html" html)))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "./runtests.py" "-vv" "--no-build" "--mode=fast"
"-j" (number->string (parallel-job-count)))))))))
(propagated-inputs (list python-numpy python-matplotlib python-pyparsing))
(inputs (list openblas pybind11))
(native-inputs
(list gfortran
perl
python-cython
python-numpydoc
python-pydata-sphinx-theme
python-pytest
python-pytest-xdist
python-sphinx
python-sphinx-panels
python-threadpoolctl
which))
(home-page "https://scipy.org/")
(synopsis "The Scipy library provides efficient numerical routines")
(description "The SciPy library is one of the core packages that make up
the SciPy stack. It provides many user-friendly and efficient numerical
routines such as routines for numerical integration and optimization.")
(properties `((python2-variant . ,(delay python2-scipy))))
(license license:bsd-3)))
;; Version 1.2.2 is the last version to support Python 2
(define-public python2-scipy
(package
(inherit (package-with-python2
(strip-python2-variant python-scipy)))
(version "1.2.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scipy" version))
(sha256
(base32
"1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))
(native-inputs
(list python2-cython
python2-pytest
python2-sphinx
python2-numpydoc
gfortran-7
gcc-7
perl
which))))
(define-public python2-weave
(package
(name "python2-weave")
(version "0.16.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "weave" version))
(sha256
(base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "nosetests" "-v"
"--exclude"
"test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
(propagated-inputs
(list python2-numpy))
(native-inputs
(list python2-nose))
(home-page "https://www.scipy.org/")
(synopsis "Tools for including C/C++ code within Python code")
(description "Weave is the stand-alone version of the obsolete Scipy
submodule @code{scipy.weave}. It is Python 2.x only, and is provided for
users that need new versions of Scipy but have existing code that still
depends on @code{scipy.weave}. For new code, users are recommended to use
Cython.")
(license license:bsd-3)))
(define-public python-scikit-fuzzy
(package
(name "python-scikit-fuzzy")
(version "0.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scikit-fuzzy" version))
(sha256
(base32 "0bp1n771fj44kdp7a00bcvfwirvv2rc803b7g6yf3va7v0j29c8s"))))
(build-system python-build-system)
(arguments '(#:tests? #f)) ;XXX: not compatible with newer numpy.testing
(native-inputs
(list python-nose))
(propagated-inputs
(list python-networkx python-numpy python-scipy))
(home-page "https://github.com/scikit-fuzzy/scikit-fuzzy")
(synopsis "Fuzzy logic toolkit for SciPy")
(description
"This package implements many useful tools for projects involving fuzzy
logic, also known as grey logic.")
(license license:bsd-3)))
(define-public python-scikit-image
(package
(name "python-scikit-image")
(version "0.19.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scikit-image" version))
(sha256
(base32 "0vc6c78780jivsg79ja0cncn1ma2wysy9fyz97kik0kg59jb8cyl"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'build 'change-home-dir
(lambda _
;; Change from /homeless-shelter to /tmp for write permission.
(setenv "HOME" "/tmp")
#t))
(replace 'build
(lambda _
(invoke "make")))
(replace 'check
(lambda _
;; The following tests require online data.
(invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k"
(string-append "not test_ndim"
" and not test_skin")))))))
;; See requirements/ for the list of build and run time requirements.
;; NOTE: scikit-image has an optional dependency on python-pooch, however
;; propagating it would enable many more tests that require online data.
(propagated-inputs
(list python-cloudpickle
python-dask
python-imageio
python-matplotlib
python-networkx
python-numpy
python-pillow
python-pythran
python-pywavelets
python-scipy
python-tifffile))
(native-inputs
(list python-cython
python-pytest
python-pytest-localserver))
(home-page "https://scikit-image.org/")
(synopsis "Image processing in Python")
(description
"Scikit-image is a collection of algorithms for image processing.")
(license license:bsd-3)))
(define-public python-scikit-allel
(package
(name "python-scikit-allel")
(version "1.3.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scikit-allel" version))
(sha256
(base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "setup.py" "build_ext" "--inplace")
(invoke "python" "-m" "pytest" "-v" "allel"
;; AttributeError: 'Dataset' object has no attribute 'asstr'
"-k" (string-append
"not test_vcf_to_hdf5"
" and not test_vcf_to_hdf5_exclude"
" and not test_vcf_to_hdf5_rename"
" and not test_vcf_to_hdf5_group"
" and not test_vcf_to_hdf5_ann"))))))))
(propagated-inputs
(list python-dask
python-numpy))
(native-inputs
(list python-cython
;; The following are all needed for the tests
htslib
python-h5py
python-hmmlearn
python-numexpr
python-pytest
python-scipy
python-setuptools-scm
python-zarr))
(home-page "https://github.com/cggh/scikit-allel")
(synopsis "Explore and analyze genetic variation data")
(description
"This package provides utilities for exploratory analysis of large scale
genetic variation data.")
(license license:expat)))
(define-public python-sgp4
(package
(name "python-sgp4")
(version "2.12")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sgp4" version))
(sha256
(base32 "0dncp9i5b6afkg7f8mj9j0qzsp008b8v73yc0qkmizhpns7mvwvx"))))
(build-system python-build-system)
(propagated-inputs
(list python-numpy))
(home-page "https://github.com/brandon-rhodes/python-sgp4")
(synopsis "Track earth satellite TLE orbits using SGP4")
(description
"This package provides a Python implementation of the most recent version
of the SGP4 satellite tracking algorithm.")
(license license:expat)))
(define-public python-trimesh
(package
(name "python-trimesh")
(version "3.10.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "trimesh" version))
(sha256
(base32 "0bw55cwxlxds0j54naijh64sdb0rkscx4i1fy0ql94h96kw2p2ir"))))
(build-system python-build-system)
(propagated-inputs
(list python-numpy))
(native-inputs
(list python-coveralls
python-pyinstrument
python-pytest
python-pytest-cov))
(arguments
`(;; TODO: Get tests to work.
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-build
(lambda _
(substitute* "trimesh/resources/templates/blender_boolean.py"
(("\\$MESH_PRE")
"'$MESH_PRE'")))))))
(home-page "https://github.com/mikedh/trimesh")
(synopsis "Python library for loading and using triangular meshes")
(description
"Trimesh is a pure Python library for loading and using triangular meshes
with an emphasis on watertight surfaces. The goal of the library is to provide
a full featured and well tested Trimesh object which allows for easy
manipulation and analysis, in the style of the Polygon object in the Shapely
library.")
(license license:expat)))
(define-public python-pandas
(package
(name "python-pandas")
(version "1.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pandas" version))
(sha256
(base32 "04lsak3j5hq2hk0vfjf532rdxdqmg2akamdl4yl3qipihp2izg4j"))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build utils)
(guix build python-build-system)
(ice-9 ftw)
(srfi srfi-1)
(srfi srfi-26))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enable-parallel-build
(lambda _
(substitute* "setup.py"
(("\"-j\", type=int, default=1")
(format #f "\"-j\", type=int, default=~a"
(parallel-job-count))))))
(add-after 'unpack 'patch-which
(lambda* (#:key inputs #:allow-other-keys)
(let ((which (assoc-ref inputs "which")))
(substitute* "pandas/io/clipboard/__init__.py"
(("^WHICH_CMD = .*")
(string-append "WHICH_CMD = \"" which "\"\n"))))))
(add-before 'check 'prepare-x
(lambda _
(system "Xvfb &")
(setenv "DISPLAY" ":0")
;; xsel needs to write a log file.
(setenv "HOME" "/tmp")))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(let ((build-directory
(string-append
(getcwd) "/build/"
(first (scandir "build"
(cut string-prefix? "lib." <>))))))
(substitute* "pyproject.toml"
;; Not all data files are distributed with the tarball.
(("--strict-data-files ") ""))
(with-directory-excursion build-directory
(when tests?
(invoke "pytest" "-vv" "pandas" "--skip-slow"
"--skip-network"
"-n" (number->string (parallel-job-count))
"-k"
(string-append
;; These test access the internet (see:
;; https://github.com/pandas-dev/pandas/issues/45085).:
;; pandas/tests/io/xml/test_xml.py::test_wrong_url[lxml]
;; pandas/tests/io/xml/test_xml.py::test_wrong_url[etree]
"not test_wrong_url"
;; TODO: Missing input
" and not TestS3"
" and not s3"
;; This test fails when run with pytest-xdist
;; (see:
;; https://github.com/pandas-dev/pandas/issues/39096).
" and not test_memory_usage"))))))))))
(propagated-inputs
(list python-jinja2
python-numpy
python-openpyxl
python-pytz
python-dateutil
python-xlrd
python-xlsxwriter))
(inputs
(list which xclip xsel))
(native-inputs
(list python-cython
python-beautifulsoup4
python-lxml
python-html5lib
python-pytest
python-pytest-mock
python-pytest-xdist
;; Needed to test clipboard support.
xorg-server-for-tests))
(home-page "https://pandas.pydata.org")
(synopsis "Data structures for data analysis, time series, and statistics")
(description
"Pandas is a Python package providing fast, flexible, and expressive data
structures designed to make working with structured (tabular,
multidimensional, potentially heterogeneous) and time series data both easy
and intuitive. It aims to be the fundamental high-level building block for
doing practical, real world data analysis in Python.")
(license license:bsd-3)))
(define-public python-pythran
(package
(name "python-pythran")
(version "0.11.0")
(home-page "https://github.com/serge-sans-paille/pythran")
(source (origin
(method git-fetch)
(uri (git-reference (url home-page) (commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0cm7wfcyvkp1wmq7n1lyf2d3sj6158jf63bagjpjmfnjwij19n0p"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove bundled Boost and xsimd.
(delete-file-recursively "third_party")))))
(build-system python-build-system)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'do-not-install-third-parties
(lambda _
(substitute* "setup.py"
(("third_parties = .*")
"third_parties = []\n"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; Remove compiler flag that trips newer GCC:
;; https://github.com/serge-sans-paille/pythran/issues/908
(substitute* "pythran/tests/__init__.py"
(("'-Wno-absolute-value',")
""))
(setenv "HOME" (getcwd))
;; This setup is modelled after the upstream CI system.
(call-with-output-file ".pythranrc"
(lambda (port)
(format port "[compiler]\nblas=openblas~%")))
(invoke "pytest" "-vv"
(string-append "--numprocesses="
(number->string
(parallel-job-count)))
"pythran/tests/test_cases.py")))))))
(native-inputs
;; For tests.
(list openblas python-pytest python-pytest-xdist))
(propagated-inputs
(list boost xsimd ;headers need to be available
python-beniget python-gast python-numpy python-ply))
(synopsis "Ahead of Time compiler for numeric kernels")
(description
"Pythran is an ahead of time compiler for a subset of the Python
language, with a focus on scientific computing. It takes a Python module
annotated with a few interface descriptions and turns it into a native
Python module with the same interface, but (hopefully) faster.")
(license license:bsd-3)))
(define-public python-bottleneck
(package
(name "python-bottleneck")
(version "1.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Bottleneck" version))
(sha256
(base32 "0wz5320jx3n4q2nsvwvc7cpi66b46qbals9v53m955rmcq5ry5r0"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "python" "setup.py" "pytest"))))))
(native-inputs
(list python-hypothesis python-pytest python-pytest-runner))
(propagated-inputs
(list python-numpy))
(home-page "https://github.com/pydata/bottleneck")
(synopsis "Fast NumPy array functions written in C")
(description
"Bottleneck is a collection of fast, NaN-aware NumPy array functions
written in C.")
(license license:bsd-2)))
(define-public python-baycomp
(package
(name "python-baycomp")
(version "1.0.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "baycomp" version))
(sha256
(base32 "1c1354a7b3g8slychjgyjxqdm8z40z9kviyl9n4g9kfpdg0p4d64"))))
(build-system python-build-system)
(propagated-inputs
(list python-matplotlib python-numpy python-scipy))
(home-page "https://github.com/janezd/baycomp")
(synopsis "Library for comparison of Bayesian classifiers")
(description
"Baycomp is a library for Bayesian comparison of classifiers. Functions
in the library compare two classifiers on one or on multiple data sets. They
compute three probabilities: the probability that the first classifier has
higher scores than the second, the probability that differences are within the
region of practical equivalence (rope), or that the second classifier has
higher scores.")
(license license:expat)))
(define-public python-xarray
(package
(name "python-xarray")
(version "0.15.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "xarray" version))
(sha256
(base32
"1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
(build-system python-build-system)
(native-inputs
(list python-setuptools-scm python-pytest))
(propagated-inputs
(list python-numpy python-pandas))
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "pytest"))))))
(home-page "https://github.com/pydata/xarray")
(synopsis "N-D labeled arrays and datasets")
(description "Xarray (formerly xray) makes working with labelled
multi-dimensional arrays simple, efficient, and fun!
Xarray introduces labels in the form of dimensions, coordinates and attributes
on top of raw NumPy-like arrays, which allows for a more intuitive, more
concise, and less error-prone developer experience. The package includes a
large and growing library of domain-agnostic functions for advanced analytics
and visualization with these data structures.")
(license license:asl2.0)))
(define-public python-msgpack-numpy
(package
(name "python-msgpack-numpy")
(version "0.4.6.post0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "msgpack-numpy" version))
(sha256
(base32
"0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz"))))
(build-system python-build-system)
(propagated-inputs
(list python-msgpack python-numpy))
(home-page "https://github.com/lebedov/msgpack-numpy")
(synopsis
"Numpy data serialization using msgpack")
(description
"This package provides encoding and decoding routines that enable the
serialization and deserialization of numerical and array data types provided
by numpy using the highly efficient @code{msgpack} format. Serialization of
Python's native complex data types is also supported.")
(license license:bsd-3)))
(define-public python-ruffus
(package
(name "python-ruffus")
(version "2.8.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ruffus" version))
(sha256
(base32
"1ai673k1s94s8b6pyxai8mk17p6zvvyi87rl236fs6ls8mpdklvc"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'check)
(add-after 'install 'check
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(with-directory-excursion "ruffus/test"
(invoke "bash" "run_all_unit_tests3.cmd"))))))))
(native-inputs
(list python-pytest))
(home-page "http://www.ruffus.org.uk")
(synopsis "Light-weight computational pipeline management")
(description
"Ruffus is designed to allow scientific and other analyses to be
automated with the minimum of fuss and the least effort.")
(license license:expat)))
(define-public python-statannot
(package
(name "python-statannot")
(version "0.2.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "statannot" version))
(sha256
(base32
"1f8c2sylzr7lpjbyqxsqlp9xi8rj3d8c9hfh98x4jbb83zxc4026"))))
(build-system python-build-system)
(propagated-inputs
(list python-numpy python-seaborn python-matplotlib python-pandas
python-scipy))
(home-page
"https://github.com/webermarcolivier/statannot")
(synopsis "Add annotations to existing plots generated by seaborn")
(description
"This is a Python package to compute statistical test and add statistical
annotations on an existing boxplots and barplots generated by seaborn.")
(license license:expat)))
(define-public python-upsetplot
(package
(name "python-upsetplot")
(version "0.6.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "UpSetPlot" version))
(sha256
(base32
"11zrykwnb00w5spx4mnsnm0f9gwrphdczainpmwkyyi50vipaa2l"))
(modules '((guix build utils)))
(snippet
;; Patch for compatibility with newer setuptools:
;; https://github.com/jnothman/UpSetPlot/pull/178
'(substitute* "upsetplot/data.py"
(("import distutils")
"from distutils.version import LooseVersion")
(("if distutils\\.version\\.LooseVersion")
"if LooseVersion")))))
(build-system python-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest" "-v" "--doctest-modules")))))))
(propagated-inputs
(list python-matplotlib python-pandas))
(native-inputs
(list python-pytest-runner python-pytest-cov))
(home-page "https://upsetplot.readthedocs.io")
(synopsis "Draw UpSet plots with Pandas and Matplotlib")
(description
"This is a Python implementation of UpSet plots by Lex et al.
UpSet plots are used to visualize set overlaps; like Venn diagrams but more
readable.")
(license license:bsd-3)))
(define-public python-vedo
(package
(name "python-vedo")
(version "2022.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/marcomusy/vedo")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1hhv4xc4bphhd1zrnf7r6fpf65xvkdqmb1lh51qg1xpv91h2az0h"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-tests
;; These tests require online data.
(lambda _
(substitute* "tests/common/test_actors.py"
(("^st = .*") "")
(("^assert isinstance\\(st\\.GetTexture\\(\\), .*") ""))
(delete-file "tests/common/test_pyplot.py")))
(add-after 'build 'mpi-setup
,%openmpi-setup)
(replace 'check
(lambda* (#:key tests? inputs outputs #:allow-other-keys)
(when tests?
(setenv "HOME" (getcwd))
(add-installed-pythonpath inputs outputs)
(with-directory-excursion "tests"
(for-each (lambda (dir)
(with-directory-excursion dir
(invoke "./run_all.sh")))
'("common" "dolfin"))))))
;; Disable the sanity check, which fails with the following error:
;;
;; ...checking requirements: ERROR: vedo==2022.2.0 DistributionNotFound(Requirement.parse('vtk<9.1.0'), {'vedo'})
(delete 'sanity-check))))
(native-inputs
(list pkg-config
python-pkgconfig))
(propagated-inputs
(list fenics
python-deprecated
python-matplotlib
python-numpy
vtk))
(home-page "https://github.com/marcomusy/vedo")
(synopsis
"Analysis and visualization of 3D objects and point clouds")
(description
"@code{vedo} is a fast and lightweight python module for
scientific analysis and visualization. The package provides a wide
range of functionalities for working with three-dimensional meshes and
point clouds. It can also be used to generate high quality
two-dimensional renderings such as scatter plots and histograms.
@code{vedo} is based on @code{vtk} and @code{numpy}.")
;; vedo is released under the Expat license. Included fonts are
;; covered by the OFL license and textures by the CC0 license.
;; The earth images are in the public domain.
(license (list license:expat
license:silofl1.1
license:cc0
license:public-domain))))
(define-public python-pandas-flavor
(package
(name "python-pandas-flavor")
(version "0.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pandas_flavor" version))
(sha256
(base32
"12g4av8gpl6l83yza3h97j3f2jblqv69frlidrvdq8ny2rc6awbq"))))
(build-system python-build-system)
(propagated-inputs
(list python-pandas python-xarray))
(home-page "https://github.com/Zsailer/pandas_flavor")
(synopsis "Write your own flavor of Pandas")
(description "Pandas 0.23 added a simple API for registering accessors
with Pandas objects. Pandas-flavor extends Pandas' extension API by
@itemize
@item adding support for registering methods as well
@item making each of these functions backwards compatible with older versions
of Pandas
@end itemize")
(license license:expat)))
(define-public python-pingouin
(package
(name "python-pingouin")
(version "0.5.1")
(source
;; The PyPI tarball does not contain the tests.
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/raphaelvallat/pingouin")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"10v3mwcmyc7rd2957cbmfcw66yw2y0fz7zcfyx46q8slbmd1d8d4"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; On loading, Pingouin uses the outdated package to check if a newer
;; version is available on PyPI. This check adds an extra dependency
;; and is irrelevant to Guix users. So, disable it.
(add-after 'unpack 'remove-outdated-check
(lambda _
(substitute* "setup.py"
(("'outdated',") ""))
(substitute* "pingouin/__init__.py"
(("^from outdated[^\n]*") "")
(("^warn_if_outdated[^\n]*") ""))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest")))))))
(native-inputs
(list python-pytest python-pytest-cov))
(propagated-inputs
(list python-matplotlib
python-mpmath
python-numpy
python-pandas
python-pandas-flavor
python-scikit-learn
python-scipy
python-seaborn
python-statsmodels
python-tabulate))
(home-page "https://pingouin-stats.org/")
(synopsis "Statistical package for Python")
(description "Pingouin is a statistical package written in Python 3 and
based mostly on Pandas and NumPy. Its features include
@itemize
@item ANOVAs: N-ways, repeated measures, mixed, ancova
@item Pairwise post-hocs tests (parametric and non-parametric) and pairwise
correlations
@item Robust, partial, distance and repeated measures correlations
@item Linear/logistic regression and mediation analysis
@item Bayes Factors
@item Multivariate tests
@item Reliability and consistency
@item Effect sizes and power analysis
@item Parametric/bootstrapped confidence intervals around an effect size or a
correlation coefficient
@item Circular statistics
@item Chi-squared tests
@item Plotting: Bland-Altman plot, Q-Q plot, paired plot, robust correlation,
and more
@end itemize")
(license license:gpl3)))
(define-public python-distributed
(package
(name "python-distributed")
(version "2022.05.2")
(source
(origin
;; The test files are not included in the archive on pypi
(method git-fetch)
(uri (git-reference
(url "https://github.com/dask/distributed")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"009jrlk7kmazrd3nkl217cl3x5ddg7kw9mqdgq1z9knv5h1rm8qv"))
;; Delete bundled copy of python-versioneer.
(snippet '(delete-file "versioneer.py"))))
(build-system python-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'versioneer
(lambda _
(invoke "versioneer" "install")))
(add-after 'unpack 'fix-references
(lambda* (#:key outputs #:allow-other-keys)
(substitute* '("distributed/comm/tests/test_ucx_config.py"
"distributed/tests/test_client.py"
"distributed/tests/test_queues.py"
"distributed/tests/test_variable.py"
"distributed/cli/tests/test_tls_cli.py"
"distributed/cli/tests/test_dask_spec.py"
"distributed/cli/tests/test_dask_worker.py"
"distributed/cli/tests/test_dask_scheduler.py")
(("\"dask-scheduler\"")
(format #false "\"~a/bin/dask-scheduler\""
(assoc-ref outputs "out")))
(("\"dask-worker\"")
(format #false "\"~a/bin/dask-worker\""
(assoc-ref outputs "out"))))))
;; ERROR: distributed==2022.5.2
;; ContextualVersionConflict (locket 0.2.0
;; (/gnu/store/...-python-locket-0.2.0/lib/python3.9/site-packages),
;; Requirement.parse('locket>=1.0.0'), {'distributed'})
(delete 'sanity-check)
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "DISABLE_IPV6" "1")
;; The integration tests are all problematic to some
;; degree. They either require network access or some
;; other setup. We only run the tests in
;; distributed/tests.
(for-each (lambda (dir)
(delete-file-recursively
(string-append "distributed/" dir "/tests")))
(list "cli" "comm" "dashboard" "deploy" "diagnostics"
"http" "http/scheduler" "http/worker"
"protocol" "shuffle"))
(invoke "python" "-m" "pytest" "-vv" "distributed"
"-m"
(string-append "not slow"
" and not flaky"
" and not gpu"
" and not ipython"
" and not avoid_ci")
"-k"
(string-append
;; These fail because they require network access,
;; specifically access to 8.8.8.8.
"not "
(string-join
(list
"TestClientSecurityLoader.test_security_loader"
"test_BatchedSend"
"test_allowed_failures_config"
"test_async_context_manager"
"test_async_with"
"test_client_repr_closed_sync"
"test_close_closed"
"test_close_fast_without_active_handlers"
"test_close_grace_period_for_handlers"
"test_close_loop_sync"
"test_close_properly"
"test_close_twice"
"test_compression"
"test_connection_pool"
"test_connection_pool_close_while_connecting"
"test_connection_pool_detects_remote_close"
"test_connection_pool_outside_cancellation"
"test_connection_pool_remove"
"test_connection_pool_respects_limit"
"test_connection_pool_tls"
"test_counters"
"test_dashboard_host"
"test_dashboard_link_cluster"
"test_dashboard_link_inproc"
"test_deserialize_error"
"test_dont_override_default_get"
"test_errors"
"test_fail_to_pickle_target_2"
"test_file_descriptors_dont_leak"
"test_finished"
"test_get_client_functions_spawn_clusters"
"test_host_uses_scheduler_protocol"
"test_identity_inproc"
"test_identity_tcp"
"test_large_packets_inproc"
"test_locked_comm_drop_in_replacement"
"test_locked_comm_intercept_read"
"test_locked_comm_intercept_write"
"test_multiple_listeners"
"test_no_dangling_asyncio_tasks"
"test_plugin_exception"
"test_plugin_internal_exception"
"test_plugin_multiple_exceptions"
"test_ports"
"test_preload_import_time"
"test_queue_in_task"
"test_quiet_client_close"
"test_rebalance_sync"
"test_repr_localcluster"
"test_require_encryption"
"test_rpc_default"
"test_rpc_inproc"
"test_rpc_message_lifetime_default"
"test_rpc_message_lifetime_inproc"
"test_rpc_message_lifetime_tcp"
"test_rpc_serialization"
"test_rpc_tcp"
"test_rpc_tls"
"test_rpc_with_many_connections_inproc"
"test_rpc_with_many_connections_tcp"
"test_scheduler_file"
"test_security_dict_input_no_security"
"test_security_loader"
"test_security_loader_ignored_if_explicit_security_provided"
"test_security_loader_ignored_if_returns_none"
"test_send_after_stream_start"
"test_send_before_close"
"test_send_before_start"
"test_send_recv_args"
"test_send_recv_cancelled"
"test_sending_traffic_jam"
"test_serializers"
"test_server"
"test_server_comms_mark_active_handlers"
"test_shutdown"
"test_shutdown_localcluster"
"test_teardown_failure_doesnt_crash_scheduler"
"test_threadpoolworkers_pick_correct_ioloop"
"test_tls_listen_connect"
"test_tls_temporary_credentials_functional"
"test_variable_in_task"
"test_worker_preload_text"
"test_worker_uses_same_host_as_nanny")
" and not ")
;; These fail because it doesn't find dask[distributed]
" and not test_quiet_close_process"
;; This one fails because of a silly assert failure:
;; '2022.05.2' == '2022.5.2'
" and not test_version"
" and not test_git_revision"
;; Recursion stack failure. No idea what they
;; expected to happen.
" and not test_stack_overflow"
;; These tests are rather flaky
" and not test_quiet_quit_when_cluster_leaves"
" and not multiple_clients_restart"))))))))
(propagated-inputs
(list python-click
python-cloudpickle
python-cryptography
python-dask
python-msgpack
python-psutil
python-pyyaml
python-setuptools
python-sortedcontainers
python-tblib
python-toolz
python-tornado-6
python-urllib3
python-zict))
(native-inputs
(list python-pytest
python-pytest-timeout
python-flaky
python-versioneer))
(home-page "https://distributed.dask.org")
(synopsis "Distributed scheduler for Dask")
(description "Dask.distributed is a lightweight library for distributed
computing in Python. It extends both the @code{concurrent.futures} and
@code{dask} APIs to moderate sized clusters.")
(license license:bsd-3)))
(define-public python-modin
(package
(name "python-modin")
(version "0.10.1")
(source
(origin
;; The archive on pypi does not include all required files.
(method git-fetch)
(uri (git-reference
(url "https://github.com/modin-project/modin")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"128ghfb9ncmnn8km409xjcdppvn9nr9jqw8rkvsfavh7wnwlk509"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'make-files-writable
(lambda _
(for-each make-file-writable (find-files "."))))
(add-after 'unpack 'loosen-requirements
(lambda _
(substitute* "setup.py"
;; Don't depend on a specific version of Pandas.
(("pandas==")
"pandas>="))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(setenv "MODIN_ENGINE" "dask")
(invoke "python" "-m" "pytest"
"modin/pandas/test/test_concat.py")
(setenv "MODIN_ENGINE" "python")
(invoke "python" "-m" "pytest"
"modin/pandas/test/test_concat.py")))))))
(propagated-inputs
(list python-cloudpickle
python-dask
python-distributed
python-numpy
python-packaging
python-pandas))
(native-inputs
(list python-coverage
python-jinja2
python-lxml
python-matplotlib
python-msgpack
python-openpyxl
python-psutil
python-pyarrow
python-pytest
python-pytest-benchmark
python-pytest-cov
python-pytest-xdist
python-scipy
python-sqlalchemy
python-tables
python-tqdm
python-xarray
python-xlrd))
(home-page "https://github.com/modin-project/modin")
(synopsis "Make your pandas code run faster")
(description
"Modin uses Ray or Dask to provide an effortless way to speed up your
pandas notebooks, scripts, and libraries. Unlike other distributed DataFrame
libraries, Modin provides seamless integration and compatibility with existing
pandas code.")
(license license:asl2.0)))
(define-public python-numpy-groupies
(package
(name "python-numpy-groupies")
(version "0.9.14")
(source
(origin
(method url-fetch)
(uri (pypi-uri "numpy_groupies" version))
(sha256
(base32 "000qz0z78rs3l6y0dd2vzvd2lx3mczm2762whwsdnhz6c35axdq1"))))
(build-system python-build-system)
(native-inputs
(list python-pytest
python-pytest-runner
python-numba
python-numpy))
(home-page "https://github.com/ml31415/numpy-groupies")
(synopsis "Tools for group-indexing operations: aggregated sum and more")
(description
"This package provides optimized tools for group-indexing operations:
aggregated sum and more.")
(license license:bsd-3)))
(define-public python-pyvista
(package
(name "python-pyvista")
(version "0.34.0")
(source
;; The PyPI tarball does not contain the tests.
;; (However, we don't yet actually run the tests.)
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pyvista/pyvista")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0f2x2wvi5pkpv5h3jrnx8zxnaj51navfqp2fdna1l9rpjgjjf94g"))))
(build-system python-build-system)
(propagated-inputs
(list python-appdirs
python-imageio
python-matplotlib
python-meshio
python-numpy
python-pillow
python-scooby
vtk))
(arguments
'(#:phases
(modify-phases %standard-phases
;; Disable tests for now because they require several modules
;; currently unpackaged in Guix.
(delete 'check)
;; Disable the sanity check, which fails with the following error:
;;
;; ...checking requirements: ERROR: pyvista==0.34.0 DistributionNotFound(Requirement.parse('vtk'), {'pyvista'})
(delete 'sanity-check))))
(home-page "https://docs.pyvista.org/")
(synopsis "3D plotting and mesh analysis through VTK")
(description
"PyVista is...
@itemize
@item @emph{Pythonic VTK}: a high-level API to the Visualization
Toolkit (VTK);
@item mesh data structures and filtering methods for spatial datasets;
@item 3D plotting made simple and built for large/complex data geometries.
@end itemize
This package provides a Pythonic, well-documented interface exposing VTK's
powerful visualization backend to facilitate rapid prototyping, analysis, and
visual integration of spatially referenced datasets.")
(license license:expat)))
(define-public python-traittypes
(package
(name "python-traittypes")
(version "0.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "traittypes" version))
(sha256
(base32 "1mlv93irdrgxrhnhq3ksi9585d55bpi4mv9dha4p8gkkjiia4vxy"))))
(build-system python-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; This one test fails because it doesn't raise an expected
;; exception.
(invoke "pytest" "-vv" "-k" "not test_bad_values")))))))
(propagated-inputs (list python-traitlets))
(native-inputs
(list python-numpy
python-pandas
python-nose
python-pytest
python-xarray))
(home-page "https://github.com/jupyter-widgets/traittypes")
(synopsis "Trait types for NumPy, SciPy and friends")
(description "The goal of this package is to provide a reference
implementation of trait types for common data structures used in the scipy
stack such as numpy arrays or pandas and xarray data structures. These are
out of the scope of the main traitlets project but are a common requirement to
build applications with traitlets in combination with the scipy stack.")
(license license:bsd-3)))
(define-public python-aplus
(package
(name "python-aplus")
(version "0.11.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "aplus" version))
(sha256
(base32 "1rznc26nlp641rn8gpdngfp79a3fji38yavqakxi35mx2da04msg"))))
(build-system python-build-system)
(home-page "https://github.com/xogeny/aplus")
(synopsis "Promises/A+ for Python")
(description "This package is an implementation of the Promises/A+
specification and test suite in Python.")
(license license:expat)))
(define-public python-climin
(package
(name "python-climin")
(version "0.1a1")
(source (origin
(method url-fetch)
(uri (pypi-uri "climin" version))
(sha256
(base32
"1wpjisd5zzi5yvjff02hnxn84822k8sdxvvd33lil2x79wdb36rv"))))
(build-system python-build-system)
(native-inputs (list python-nose))
(propagated-inputs (list python-numpydoc python-numpy python-scipy))
(home-page "https://github.com/BRML/climin")
(synopsis "Optimization for machine learning")
(description
"@command{climin} is a Python package for optimization,
heavily biased to machine learning scenarios. It works on top of
@command{numpy} and (partially) @command{gnumpy}.")
(license license:bsd-3)))
(define-public python-paramz
(package
(name "python-paramz")
(version "0.9.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "paramz" version))
(sha256
(base32
"16hbh97kj6b1c2gw22rqnr3w3nqkszh9gj8vgx738gq81wf225q9"))))
(build-system python-build-system)
(propagated-inputs (list python-decorator python-numpy python-scipy
python-six))
(home-page "https://github.com/sods/paramz")
(synopsis "The Parameterization Framework")
(description
"@command{paramz} is a lightweight parameterization framework
for parameterized model creation and handling. Its features include:
@itemize
@item Easy model creation with parameters.
@item Fast optimized access of parameters for optimization routines.
@item Memory efficient storage of parameters (only one copy in memory).
@item Renaming of parameters.
@item Intuitive printing of models and parameters.
@item Gradient saving directly inside parameters.
@item Gradient checking of parameters.
@item Optimization of parameters.
@item Jupyter notebook integration.
@item Efficient storage of models, for reloading.
@item Efficient caching.
@end itemize")
(license license:bsd-3)))
(define-public python-gpy
(package
(name "python-gpy")
(version "1.10.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "GPy" version))
(sha256
(base32
"1yx65ajrmqp02ykclhlb0n8s3bx5r0xj075swwwigiqaippr7dx2"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
(add-before 'check 'remove-plotting-tests
;; These fail
(lambda _
(delete-file "GPy/testing/plotting_tests.py"))))))
(native-inputs (list python-cython python-nose python-climin))
(propagated-inputs (list python-numpy python-paramz python-scipy
python-six))
(home-page "https://sheffieldml.github.io/GPy/")
(synopsis "The Gaussian Process Toolbox")
(description
"@command{GPy} is a Gaussian Process (GP) framework written in
Python, from the Sheffield machine learning group. GPy implements a range of
machine learning algorithms based on GPs.")
(license license:bsd-3)))
|