summary refs log tree commit diff
path: root/gnu/packages/sagemath.scm
blob: b96cb6b96ed17ad422429814ee0a4f3f289b5ca2 (plain) (blame)
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
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages sagemath)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bdw-gc)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages image)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz))


(define-public python-cypari2
  (package
    (name "python-cypari2")
    (version "2.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cypari2" version))
       (sha256
        (base32
         "1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-cython" ,python-cython)))
    (propagated-inputs
     `(("python-cysignals" ,python-cysignals)))
    (inputs
     `(("gmp" ,gmp)
       ("pari-gp", pari-gp)))
    (home-page "https://cypari2.readthedocs.io/")
    (synopsis
     "Python interface to the number theory library libpari")
    (description
     "Cypari2 provides a Python interface to the number theory library
PARI/GP.  It has been spun off from the SageMath mathematics software system,
but it can be used independently.")
    (license license:gpl2+)))

(define-public python2-cypari2
  (package-with-python2 python-cypari2))

;; The stable version of the following package is not young enough to be
;; used with Sage, since it does not support cython; so we use a beta
;; release.
(define-public python-gmpy2
  (package
    (name "python-gmpy2")
    (version "2.1.0b1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/aleaxit/gmpy")
                    (commit (string-append "gmpy2-" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97"))))
    (build-system python-build-system)
    (native-inputs
     `(("unzip" ,unzip)))
    (inputs
     `(("gmp" ,gmp)
       ("mpfr" ,mpfr)
       ("mpc" ,mpc)))
    (home-page "https://github.com/aleaxit/gmpy")
    (synopsis
     "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x")
    (description
     "This package provides a Python interface to the GNU multiprecision
libraries GMO, MPFR and MPC.")
    (license license:lgpl3+)))

(define-public python2-gmpy2
  (package-with-python2 python-gmpy2))

(define-public cliquer
  (package
    (name "cliquer")
    (version "1.21")
    ;; The original source package is available from the home page and
    ;; has not seen any release since 2010; it comes with only a Makefile
    ;; without an "install" target. Instead, there is an autotoolized
    ;; tarball available from the Sage project.
    (source
     (origin
       (method url-fetch)
       (uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
       (sha256
        (base32
         "1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
    (build-system gnu-build-system)
    (synopsis "C routines for finding cliques in weighted graphs")
    (description "Cliquer is a set of reentrant C routines for finding
cliques in a weighted or unweighted graph.  It uses an exact
branch-and-bound algorithm.  It can search for maximum or maximum-weight
cliques or cliques with size or weight within a given range, restrict the
search to maximal cliques, store cliques in memory and call a user-defined
function for every found clique.")
    (license license:gpl2+)
    (home-page "https://users.aalto.fi/~pat/cliquer.html")))

(define-public libbraiding
  (package
    (name "libbraiding")
    (version "1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url (string-append "https://github.com/miguelmarco/"
                                  name))
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (synopsis "Computations with braid groups")
    (description "libbraiding performs computations with braid groups,
in particular it computes normal forms of group elements.")
    (license license:gpl2+)
    (home-page "https://github.com/miguelmarco/libbraiding")))

(define-public libhomfly
  (package
    (name "libhomfly")
    (version "1.02r6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url (string-append "https://github.com/miguelmarco/"
                                  name))
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (inputs
     `(("libgc" ,libgc)))
    (synopsis "Computation of homfly polynomials of links")
    (description "libhomfly computes homfly polynomials of links,
represented as strings.")
    (license license:public-domain)
    (home-page "https://github.com/miguelmarco/libhomfly")))

;; The following three packages from the Linbox group are needed in
;; an outdated version for Sage.

(define-public givaro-4.0.4
  (package (inherit givaro)
    (name "givaro")
    (version "4.0.4")
    (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
                "199p8wyj5i63jbnk7j8qbdbfp5rm2lpmcxyk3mdjy9bz7ygx3hhy"))))))

(define-public fflas-ffpack-2.3.2
  (package (inherit fflas-ffpack)
    (name "fflas-ffpack")
    (version "2.3.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/linbox-team/fflas-ffpack")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1cqhassj2dny3gx0iywvmnpq8ca0d6m82xl5rz4mb8gaxr2kwddl"))))
    (propagated-inputs
     `(("givaro" ,givaro-4.0.4)))
    ;; A test fails, but since all tests pass in the latest version,
    ;; there is not much point in investigating.
    (arguments
     (substitute-keyword-arguments (package-arguments fflas-ffpack)
       ((#:tests? _ #f) #f)))))

(define-public linbox-1.5.2
  (package (inherit linbox)
    (version "1.5.2")
    (name "linbox")
    (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
                "1wfivlwp30mzdy1697w7rzb8caajim50mc8h27k82yipn2qc5n4i"))))
    (inputs
     `(("fflas-ffpack" ,fflas-ffpack-2.3.2)))))

(define-public pynac
  (package
    (name "pynac")
    (version "0.7.26")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/pynac/pynac/")
              (commit (string-append "pynac-" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("flint" ,flint)
       ("gmp" ,gmp)
       ("python" ,python)
       ("singular" ,singular)))
    (synopsis "Sage fork of GiNaC")
    (description "Pynac is a derivative of the C++ library GiNaC, which
allows manipulation of symbolic expressions.  It currently provides the
backend for symbolic expressions in Sage.  The main difference between
Pynac and GiNaC is that Pynac relies on Sage to provide the operations
on numerical types, while GiNaC depends on CLN for this purpose.")
    (license license:gpl2+)
    (home-page "http://pynac.org/")))

;; Sage has become upstream of the following package.
(define-public zn-poly
  (package
    (name "zn-poly")
    (version "0.9.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url (string-append "https://gitlab.com/sagemath/"
                                  "zn_poly.git/"))
              (commit version)))
       (file-name (git-file-name "zn_poly" version))
       (sha256
        (base32 "1wbc3apxcldxfcw1dnwnn7fvlfb6bwvlr8glvgv6hf79p9r2s4j0"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("python" ,python-2)))
    (inputs
     `(("gmp" ,gmp)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'configure
           ;; The configure script chokes on --enable-fast-install.
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (invoke "./configure"
                     (string-append "--prefix=" (assoc-ref outputs "out"))
                     "--cflags=-O3 -fPIC")))
         (add-before 'build 'prepare-build
           (lambda _
             (setenv "CC" "gcc")
             #t))
         (add-after 'build 'build-so
           (lambda _
             (invoke "make" "libzn_poly.so")))
         (add-after 'install 'install-so
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (lib (string-append out "/lib"))
                    (soname (string-append "libzn_poly-" ,version ".so"))
                    (target (string-append lib "/" soname)))
               (install-file "libzn_poly.a" lib)
               (install-file soname lib)
               (symlink target
                        (string-append lib "/libzn_poly.so"))
               (symlink target
                        (string-append lib "/libzn_poly-"
                                       ,(version-major+minor version)
                                       ".so")))
             #t)))))
    (synopsis "Arithmetic for polynomials over Z/NZ")
    (description "zn_poly implements the arithmetic of polynomials the
coefficients of which are modular integers.")
    (license (list license:gpl2 license:gpl3)) ; dual licensed
    (home-page "https://gitlab.com/sagemath/zn_poly")))

(define-public brial
  (package
    (name "brial")
    (version "1.2.8")
    (source
    (origin
      (method git-fetch)
      (uri (git-reference
             (url "https://github.com/BRiAl/BRiAl/")
             (commit version)))
      (file-name (git-file-name name version))
      (sha256
       (base32 "0qhgckd4fvbs40jw14mvw89rccv94d3df27kipd27hxd4cx7y80y"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)
       ("pkg-config" ,pkg-config)))
    (inputs
     `(("boost" ,boost)
       ("libpng" ,libpng)
       ("m4ri" ,m4ri)))
    (arguments
    ;; We are missing the boost unit test framework.
     `(#:tests? #f
       #:configure-flags (list "--without-boost-unit-test-framework")))
    (synopsis "Arithmetic of polynomials over boolean rings")
    (description "BRiAl is the successor to  PolyBoRi maintained by the
Sage community.  Its core is a C++ library, which provides high-level data
types for Boolean polynomials and monomials, exponent vectors, as well as
for the underlying polynomial rings and subsets of the powerset of the
Boolean variables.  As a unique approach, binary decision diagrams are
used as internal storage type for polynomial structures.")
    (license license:gpl2+)
    (home-page "https://github.com/BRiAl/BRiAl/")))

(define-public lcalc
  (package
    (name "lcalc")
    (version "1.23")
    ;; The original home page of the project has disappeared, as well as
    ;; code hosted by the original author on Google Code. The latter has
    ;; been copied to gitlab.com/sagemath and purportedly contains patches
    ;; for a never released version 1.3, that supposedly follows 1.23.
    ;; We use the tarball as well as the patches hosted inside the sage
    ;; package system distributed with the sage tarball.
    (source
     (origin
       (method url-fetch)
       (uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/"
                           "upstream/lcalc/lcalc-1.23.tar.bz2"))
       (sha256
        (base32
         "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"))
       (patches (search-patches "lcalc-lcommon-h.patch"
                                "lcalc-default-parameters-1.patch"
                                "lcalc-default-parameters-2.patch"
                                "lcalc-using-namespace-std.patch"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no tests
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (add-before 'build 'prepare-build
           (lambda* (#:key outputs #:allow-other-keys)
             (chdir "src")
             (let ((out (assoc-ref outputs "out")))
               (substitute* "Makefile"
                 (("^INSTALL_DIR= /usr/local")
                  (string-append "INSTALL_DIR=" out))
                 ;; Sage renames the include directory, so we do it also.
                 (("include/Lfunction")
                  "include/libLfunction")))
             #t))
         (add-before 'install 'make-output-dirs
           (lambda* (#:key outputs #:allow-other-keys)
             (let* ((out (assoc-ref outputs "out"))
                    (bin (string-append out "/bin"))
                    (lib (string-append out "/lib"))
                    (include (string-append out "/include")))
               (mkdir-p bin)
               (mkdir-p lib)
               (mkdir-p include))
             #t)))))
    ;; FIXME:
    ;; We need to add pari-gp and probably pari related patches from the
    ;; sage project, as well as uncomment the line setting PARI_DEFINE in
    ;; the Makefile to get the full functionality of this package.
    ;; For the time being, we hope that sage can be compiled without.
    (synopsis "C++ library for L-functions")
    (description "Lcalc computes L-functions, in particular the Riemann
zeta function and its twists by quadratic characters.")
    (license license:gpl2+)
    (home-page "https://gitlab.com/sagemath/sage")))

(define-public ratpoints
  (package
    (name "ratpoints")
    (version "2.1.3")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://www.mathe2.uni-bayreuth.de/stoll/programs/"
                    "ratpoints-" version ".tar.gz"))
              (sha256
               (base32
                "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
              (patches
               ;; Taken from
               ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
               (search-patches "ratpoints-sturm_and_rp_private.patch"))))
    (build-system gnu-build-system)
    (arguments
     `(#:test-target "test"
       #:make-flags
       (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))
             "CCFLAGS=-fPIC")
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)            ;no configure script
         (add-before 'install 'create-install-directories
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               (mkdir-p out)
               (with-directory-excursion out
                 (for-each (lambda (d) (mkdir-p d))
                           '("bin" "include" "lib"))))
             #t)))))
    (inputs
     `(("gmp" ,gmp)))
    (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
    (synopsis "Find rational points on hyperelliptic curves")
    (description "Ratpoints tries to find all rational points within
a given height bound on a hyperelliptic curve in a very efficient way,
by using an optimized quadratic sieve algorithm.")
    (license license:gpl2+)))