Commit | Line | Data |
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233e7676 | 1 | ;;; GNU Guix --- Functional package management for GNU |
3f074a21 | 2 | ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr> |
4b0bf990 | 3 | ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org> |
7f055a0a | 4 | ;;; Copyright © 2016, 2017, 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr> |
69d5909e | 5 | ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org> |
67f39dd5 | 6 | ;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
ecc5bc33 | 7 | ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> |
ff6807dc | 8 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
f71f29ca | 9 | ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com> |
eb6785cf | 10 | ;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.org> |
2ed139c4 | 11 | ;;; |
233e7676 | 12 | ;;; This file is part of GNU Guix. |
2ed139c4 | 13 | ;;; |
233e7676 | 14 | ;;; GNU Guix is free software; you can redistribute it and/or modify it |
2ed139c4 AE |
15 | ;;; under the terms of the GNU General Public License as published by |
16 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
17 | ;;; your option) any later version. | |
18 | ;;; | |
233e7676 | 19 | ;;; GNU Guix is distributed in the hope that it will be useful, but |
2ed139c4 AE |
20 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of |
21 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
22 | ;;; GNU General Public License for more details. | |
23 | ;;; | |
24 | ;;; You should have received a copy of the GNU General Public License | |
233e7676 | 25 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. |
2ed139c4 | 26 | |
1ffa7090 | 27 | (define-module (gnu packages algebra) |
59a43334 | 28 | #:use-module (gnu packages) |
14e6520e | 29 | #:use-module (gnu packages autotools) |
fdb513a7 | 30 | #:use-module (gnu packages bison) |
70770b93 | 31 | #:use-module (gnu packages check) |
10b1f688 | 32 | #:use-module (gnu packages compression) |
70770b93 | 33 | #:use-module (gnu packages cpp) |
99828fa7 | 34 | #:use-module (gnu packages documentation) |
f71f29ca | 35 | #:use-module (gnu packages ed) |
5894b604 | 36 | #:use-module (gnu packages flex) |
57497c57 NG |
37 | #:use-module (gnu packages fltk) |
38 | #:use-module (gnu packages gl) | |
aae03c48 | 39 | #:use-module (gnu packages graphviz) |
57497c57 | 40 | #:use-module (gnu packages image) |
c8d99608 | 41 | #:use-module (gnu packages java) |
aae03c48 | 42 | #:use-module (gnu packages maths) |
0fc54d4b | 43 | #:use-module (gnu packages mpi) |
5894b604 | 44 | #:use-module (gnu packages multiprecision) |
1ffa7090 | 45 | #:use-module (gnu packages perl) |
4bf9cb40 | 46 | #:use-module (gnu packages pkg-config) |
6d3896b9 | 47 | #:use-module (gnu packages pulseaudio) |
aae03c48 | 48 | #:use-module (gnu packages python) |
1d6589db | 49 | #:use-module (gnu packages python-xyz) |
5894b604 | 50 | #:use-module (gnu packages readline) |
b7194849 | 51 | #:use-module (gnu packages shells) |
8f9ac901 | 52 | #:use-module (gnu packages tex) |
f71f29ca | 53 | #:use-module (gnu packages texinfo) |
57497c57 | 54 | #:use-module (gnu packages xiph) |
fb8d1be8 | 55 | #:use-module (gnu packages xorg) |
c8d99608 | 56 | #:use-module (guix build-system ant) |
7569c5cb | 57 | #:use-module (guix build-system gnu) |
8f4b1dfb | 58 | #:use-module (guix build-system cmake) |
1d6589db | 59 | #:use-module (guix build-system python) |
5894b604 | 60 | #:use-module (guix download) |
c8d99608 | 61 | #:use-module (guix git-download) |
697eb65d | 62 | #:use-module (guix hg-download) |
5894b604 TGR |
63 | #:use-module ((guix licenses) #:prefix license:) |
64 | #:use-module (guix packages) | |
7569c5cb | 65 | #:use-module (guix utils)) |
2ed139c4 AE |
66 | |
67 | ||
68 | (define-public mpfrcx | |
69 | (package | |
70 | (name "mpfrcx") | |
43a776e2 | 71 | (version "0.5") |
2ed139c4 AE |
72 | (source (origin |
73 | (method url-fetch) | |
74 | (uri (string-append | |
43a776e2 | 75 | "http://www.multiprecision.org/downloads/mpfrcx-" |
2ed139c4 AE |
76 | version ".tar.gz")) |
77 | (sha256 | |
78 | (base32 | |
43a776e2 | 79 | "1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs")))) |
2ed139c4 | 80 | (build-system gnu-build-system) |
878c8f3f AE |
81 | (propagated-inputs |
82 | `(("gmp" ,gmp) | |
83 | ("mpfr" ,mpfr) | |
84 | ("mpc" ,mpc))) ; Header files are included by mpfrcx.h. | |
35b9e423 | 85 | (synopsis "Arithmetic of polynomials over arbitrary precision numbers") |
2ed139c4 | 86 | (description |
35b9e423 | 87 | "Mpfrcx is a library for the arithmetic of univariate polynomials over |
2ed139c4 | 88 | arbitrary precision real (mpfr) or complex (mpc) numbers, without control |
35b9e423 | 89 | on the rounding. For the time being, only the few functions needed to |
2ed139c4 | 90 | implement the floating point approach to complex multiplication are |
35b9e423 | 91 | implemented. On the other hand, these comprise asymptotically fast |
e881752c | 92 | multiplication routines such as Toom–Cook and the FFT.") |
43a776e2 | 93 | (license license:lgpl3+) |
2ed139c4 AE |
94 | (home-page "http://mpfrcx.multiprecision.org/"))) |
95 | ||
10b1f688 AE |
96 | (define-public cm |
97 | (package | |
98 | (name "cm") | |
81b55bf7 | 99 | (version "0.3") |
10b1f688 AE |
100 | (source (origin |
101 | (method url-fetch) | |
102 | (uri (string-append | |
103 | "http://www.multiprecision.org/cm/download/cm-" | |
104 | version ".tar.gz")) | |
105 | (sha256 | |
106 | (base32 | |
81b55bf7 | 107 | "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc")))) |
10b1f688 AE |
108 | (build-system gnu-build-system) |
109 | (propagated-inputs | |
110 | `(("mpfrcx" ,mpfrcx) | |
111 | ("zlib" ,zlib))) ; Header files included from cm_common.h. | |
112 | (inputs | |
113 | `(("pari-gp" ,pari-gp))) | |
114 | (synopsis "CM constructions for elliptic curves") | |
115 | (description | |
116 | "The CM software implements the construction of ring class fields of | |
117 | imaginary quadratic number fields and of elliptic curves with complex | |
118 | multiplication via floating point approximations. It consists of libraries | |
119 | that can be called from within a C program and of executable command | |
120 | line applications.") | |
81b55bf7 | 121 | (license license:gpl3+) |
10b1f688 AE |
122 | (home-page "http://cm.multiprecision.org/"))) |
123 | ||
2ed139c4 AE |
124 | (define-public fplll |
125 | (package | |
126 | (name "fplll") | |
5a15ed50 | 127 | (version "4.0.4") |
2ed139c4 AE |
128 | (source (origin |
129 | (method url-fetch) | |
130 | (uri (string-append | |
131 | "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-" | |
132 | version ".tar.gz")) | |
133 | (sha256 (base32 | |
5a15ed50 | 134 | "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b")))) |
2ed139c4 AE |
135 | (build-system gnu-build-system) |
136 | (inputs `(("gmp" ,gmp) | |
137 | ("mpfr" ,mpfr))) | |
35b9e423 | 138 | (synopsis "Library for LLL-reduction of euclidean lattices") |
2ed139c4 | 139 | (description |
35b9e423 | 140 | "fplll LLL-reduces euclidean lattices. Since version 3, it can also |
2ed139c4 | 141 | solve the shortest vector problem.") |
9f51293c | 142 | (license license:lgpl2.1+) |
2ed139c4 | 143 | (home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/"))) |
4e6b699d | 144 | |
90a6d47c AE |
145 | (define-public pari-gp |
146 | (package | |
67f39dd5 RW |
147 | (name "pari-gp") |
148 | (version "2.11.1") | |
149 | (source (origin | |
150 | (method url-fetch) | |
151 | (uri (string-append | |
152 | "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-" | |
153 | version ".tar.gz")) | |
154 | (sha256 | |
155 | (base32 | |
4ebfe99a | 156 | "1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94")))) |
67f39dd5 RW |
157 | (build-system gnu-build-system) |
158 | (native-inputs | |
159 | `(("texlive" ,(texlive-union | |
160 | (list texlive-fonts-amsfonts | |
161 | texlive-latex-amsfonts))))) | |
162 | (inputs `(("gmp" ,gmp) | |
163 | ("libx11" ,libx11) | |
164 | ("perl" ,perl) | |
165 | ("readline" ,readline))) | |
166 | (arguments | |
167 | '(#:make-flags '("all") | |
168 | #:test-target "dobench" | |
169 | #:phases | |
170 | (modify-phases %standard-phases | |
171 | (replace 'configure | |
172 | (lambda* (#:key outputs #:allow-other-keys) | |
173 | (invoke "./Configure" | |
174 | (string-append "--prefix=" | |
175 | (assoc-ref outputs "out")))))))) | |
176 | (synopsis "PARI/GP, a computer algebra system for number theory") | |
177 | (description | |
178 | "PARI/GP is a widely used computer algebra system designed for fast | |
90a6d47c AE |
179 | computations in number theory (factorisations, algebraic number theory, |
180 | elliptic curves...), but it also contains a large number of other useful | |
181 | functions to compute with mathematical entities such as matrices, | |
182 | polynomials, power series, algebraic numbers, etc., and a lot of | |
183 | transcendental functions. | |
184 | PARI is also available as a C library to allow for faster computations.") | |
67f39dd5 RW |
185 | (license license:gpl2+) |
186 | (home-page "https://pari.math.u-bordeaux.fr/"))) | |
ed9f9a77 | 187 | |
f854a8c1 AE |
188 | (define-public gp2c |
189 | (package | |
190 | (name "gp2c") | |
44ff80fc | 191 | (version "0.0.11pl1") |
f854a8c1 AE |
192 | (source (origin |
193 | (method url-fetch) | |
194 | (uri (string-append | |
eeb8b0e6 | 195 | "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-" |
f854a8c1 | 196 | version ".tar.gz")) |
324bdcd8 AE |
197 | (sha256 |
198 | (base32 | |
44ff80fc | 199 | "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s")))) |
f854a8c1 | 200 | (build-system gnu-build-system) |
c67ccedd | 201 | (native-inputs `(("perl" ,perl))) |
f854a8c1 AE |
202 | (inputs `(("pari-gp" ,pari-gp))) |
203 | (arguments | |
204 | '(#:configure-flags | |
205 | (list (string-append "--with-paricfg=" | |
206 | (assoc-ref %build-inputs "pari-gp") | |
207 | "/lib/pari/pari.cfg")))) | |
208 | (synopsis "PARI/GP, a computer algebra system for number theory") | |
209 | (description | |
210 | "PARI/GP is a widely used computer algebra system designed for fast | |
211 | computations in number theory (factorisations, algebraic number theory, | |
212 | elliptic curves...), but it also contains a large number of other useful | |
213 | functions to compute with mathematical entities such as matrices, | |
214 | polynomials, power series, algebraic numbers, etc., and a lot of | |
215 | transcendental functions. | |
216 | PARI is also available as a C library to allow for faster computations. | |
217 | ||
218 | GP2C, the GP to C compiler, translates GP scripts to PARI programs.") | |
9f51293c | 219 | (license license:gpl2) |
eeb8b0e6 | 220 | (home-page "https://pari.math.u-bordeaux.fr/"))) |
f854a8c1 | 221 | |
eea7cd75 AE |
222 | (define-public cmh |
223 | (package | |
224 | (name "cmh") | |
225 | (version "1.0") | |
226 | (source (origin | |
227 | (method url-fetch) | |
228 | (uri (string-append | |
229 | "https://gforge.inria.fr/frs/download.php/33497/cmh-" | |
230 | version ".tar.gz")) | |
231 | (sha256 | |
232 | (base32 | |
233 | "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p")))) | |
234 | (build-system gnu-build-system) | |
235 | (inputs | |
236 | `(("gmp" ,gmp) | |
237 | ("mpfr" ,mpfr) | |
238 | ("mpc" ,mpc) | |
239 | ("mpfrcx" ,mpfrcx) | |
240 | ("fplll" ,fplll) | |
241 | ("pari-gp" ,pari-gp))) | |
242 | (synopsis "Igusa class polynomial computations") | |
243 | (description | |
244 | "The CMH software computes Igusa (genus 2) class polynomials, which | |
245 | parameterize the CM points in the moduli space of 2-dimensional abelian | |
246 | varieties, i.e. Jacobians of hyperelliptic curves. | |
247 | It can also be used to compute theta constants at arbitrary | |
248 | precision.") | |
249 | (license license:gpl3+) | |
250 | (home-page "http://cmh.gforge.inria.fr/"))) | |
251 | ||
7fc0e3db | 252 | (define-public giac |
57497c57 | 253 | (package |
7fc0e3db | 254 | (name "giac") |
fd4d3939 | 255 | (version "1.5.0-57") |
57497c57 NG |
256 | (source (origin |
257 | (method url-fetch) | |
258 | ;; "~parisse/giac" is not used because the maintainer regularly | |
259 | ;; overwrites the release tarball there, introducing a checksum | |
260 | ;; mismatch every time. See | |
261 | ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README> | |
262 | (uri (string-append "https://www-fourier.ujf-grenoble.fr/" | |
263 | "~parisse/debian/dists/stable/main/" | |
264 | "source/giac_" version ".tar.gz")) | |
265 | (sha256 | |
266 | (base32 | |
fd4d3939 | 267 | "08c93knsisbk9dkyyrignw0wvqbr1sa5czlvk5l307ahxbbmqncf")))) |
57497c57 NG |
268 | (build-system gnu-build-system) |
269 | (arguments | |
af90cc45 NG |
270 | `(#:modules ((ice-9 ftw) |
271 | (guix build utils) | |
272 | (guix build gnu-build-system)) | |
273 | #:phases | |
57497c57 NG |
274 | (modify-phases %standard-phases |
275 | (add-after 'unpack 'patch-bin-cp | |
90d5ec55 | 276 | ;; Some Makefiles contain hard-coded "/bin/cp". |
57497c57 | 277 | (lambda _ |
57497c57 NG |
278 | (substitute* (find-files "doc" "^Makefile") |
279 | (("/bin/cp") (which "cp"))) | |
90d5ec55 NG |
280 | #t)) |
281 | (add-after 'unpack 'disable-failing-test | |
282 | ;; FIXME: Test failing. Not sure why. | |
283 | (lambda _ | |
284 | (substitute* "check/Makefile.in" | |
285 | (("chk_fhan11") "")) | |
af90cc45 | 286 | #t)) |
9f73ac24 | 287 | (add-after 'install 'fix-doc |
af90cc45 | 288 | (lambda* (#:key outputs #:allow-other-keys) |
9f73ac24 NG |
289 | (let ((out (assoc-ref outputs "out"))) |
290 | ;; Most French documentation has a non-commercial | |
291 | ;; license, so we need to remove it. | |
292 | (with-directory-excursion (string-append out "/share/giac/doc/fr") | |
293 | (for-each delete-file-recursively | |
294 | '("cascas" "casexo" "casgeo" "casrouge" "cassim" | |
295 | "castor"))) | |
296 | ;; Remove duplicate documentation in | |
297 | ;; "%out/share/doc/giac/", where Xcas does not expect | |
298 | ;; to find it. | |
299 | (delete-file-recursively (string-append out "/share/doc/giac")) | |
300 | #t))) | |
301 | (add-after 'install 'remove-unnecessary-executable | |
302 | (lambda* (#:key outputs #:allow-other-keys) | |
303 | (let ((out (assoc-ref outputs "out"))) | |
304 | (delete-file (string-append out "/bin/xcasnew")) | |
305 | #t)))))) | |
57497c57 | 306 | (inputs |
6d3896b9 | 307 | ;;; TODO: Add libnauty. |
57497c57 | 308 | `(("fltk" ,fltk) |
6d3896b9 | 309 | ("glpk" ,glpk) |
57497c57 NG |
310 | ("gmp" ,gmp) |
311 | ("gsl" ,gsl) | |
312 | ("lapack" ,lapack) | |
313 | ("libao" ,ao) | |
314 | ("libjpeg" ,libjpeg) | |
315 | ("libpng" ,libpng) | |
6d3896b9 | 316 | ("libsamplerate" ,libsamplerate) |
57497c57 | 317 | ("libx11" ,libx11) |
99a00446 | 318 | ("libxinerama" ,libxinerama) |
57497c57 NG |
319 | ("libxft" ,libxft) |
320 | ("libxt" ,libxt) | |
321 | ("mesa" ,mesa) | |
322 | ("mpfi" ,mpfi) | |
323 | ("mpfr" ,mpfr) | |
324 | ("ntl" ,ntl) | |
325 | ("perl" ,perl) | |
326 | ("pari-gp" ,pari-gp) | |
9f73ac24 NG |
327 | ("tcsh" ,tcsh))) |
328 | (native-inputs | |
6d3896b9 NG |
329 | `(("bison" ,bison) |
330 | ("flex" ,flex) | |
331 | ("readline" ,readline) | |
a023ec6e | 332 | ("texlive" ,texlive-tiny))) |
57497c57 NG |
333 | (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html") |
334 | (synopsis "Computer algebra system") | |
335 | (description | |
336 | "Giac/Xcas is a computer algebra system. It has a compatibility mode for | |
337 | maple, mupad and the TI89. It is available as a standalone program (graphic | |
338 | or text interfaces) or as a C++ library.") | |
339 | (license license:gpl3+))) | |
340 | ||
7fc0e3db | 341 | (define-public giac-xcas |
e0f3a4fe | 342 | (deprecated-package "giac-xcas" giac)) |
7fc0e3db | 343 | |
d7ab698a AE |
344 | (define-public flint |
345 | (package | |
346 | (name "flint") | |
6c591c8e | 347 | (version "2.5.2") |
d7ab698a AE |
348 | (source (origin |
349 | (method url-fetch) | |
350 | (uri (string-append | |
351 | "http://flintlib.org/flint-" | |
352 | version ".tar.gz")) | |
353 | (sha256 (base32 | |
6c591c8e | 354 | "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb")) |
fc1adab1 | 355 | (patches (search-patches "flint-ldconfig.patch")))) |
d7ab698a | 356 | (build-system gnu-build-system) |
df15d17d | 357 | (propagated-inputs |
d7ab698a | 358 | `(("gmp" ,gmp) |
df15d17d | 359 | ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h |
d7ab698a | 360 | (arguments |
ad11974e AE |
361 | `(#:parallel-tests? #f ; seems to be necessary on arm |
362 | #:phases | |
91430de6 AE |
363 | (modify-phases %standard-phases |
364 | (replace 'configure | |
365 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
366 | (let ((out (assoc-ref outputs "out")) | |
367 | (gmp (assoc-ref inputs "gmp")) | |
368 | (mpfr (assoc-ref inputs "mpfr"))) | |
91430de6 AE |
369 | ;; do not pass "--enable-fast-install", which makes the |
370 | ;; homebrew configure process fail | |
50233d95 | 371 | (invoke "./configure" |
91430de6 AE |
372 | (string-append "--prefix=" out) |
373 | (string-append "--with-gmp=" gmp) | |
50233d95 RW |
374 | (string-append "--with-mpfr=" mpfr)) |
375 | #t)))))) | |
d7ab698a AE |
376 | (synopsis "Fast library for number theory") |
377 | (description | |
378 | "FLINT is a C library for number theory. It supports arithmetic | |
379 | with numbers, polynomials, power series and matrices over many base | |
380 | rings, including multiprecision integers and rationals, integers | |
381 | modulo n, p-adic numbers, finite fields (prime and non-prime order) | |
382 | and real and complex numbers (via the Arb extension library). | |
383 | ||
384 | Operations that can be performed include conversions, arithmetic, | |
385 | GCDs, factoring, solving linear systems, and evaluating special | |
386 | functions. In addition, FLINT provides various low-level routines for | |
387 | fast arithmetic.") | |
9f51293c | 388 | (license license:gpl2+) |
d7ab698a AE |
389 | (home-page "http://flintlib.org/"))) |
390 | ||
6b8e8285 AE |
391 | (define-public arb |
392 | (package | |
6aa54e23 | 393 | (name "arb") |
402db511 | 394 | (version "2.16.0") |
6aa54e23 RW |
395 | (source (origin |
396 | (method git-fetch) | |
397 | (uri (git-reference | |
398 | (url "https://github.com/fredrik-johansson/arb.git") | |
399 | (commit version))) | |
400 | (file-name (git-file-name name version)) | |
401 | (sha256 | |
402 | (base32 | |
402db511 | 403 | "0478671wfwy3gl26sbxh1jq1ih36z4k72waa8y2y2lvn649gb7cd")))) |
6aa54e23 RW |
404 | (build-system gnu-build-system) |
405 | (propagated-inputs | |
406 | `(("flint" ,flint))) ; flint.h is included by arf.h | |
407 | (inputs | |
408 | `(("gmp" ,gmp) | |
409 | ("mpfr" ,mpfr))) | |
410 | (arguments | |
411 | `(#:phases | |
412 | (modify-phases %standard-phases | |
413 | (replace 'configure | |
414 | (lambda* (#:key inputs outputs #:allow-other-keys) | |
415 | (let ((out (assoc-ref outputs "out")) | |
416 | (flint (assoc-ref inputs "flint")) | |
417 | (gmp (assoc-ref inputs "gmp")) | |
418 | (mpfr (assoc-ref inputs "mpfr"))) | |
419 | ;; do not pass "--enable-fast-install", which makes the | |
420 | ;; homebrew configure process fail | |
421 | (invoke "./configure" | |
422 | (string-append "--prefix=" out) | |
423 | (string-append "--with-flint=" flint) | |
424 | (string-append "--with-gmp=" gmp) | |
425 | (string-append "--with-mpfr=" mpfr)))))))) | |
426 | (synopsis "Arbitrary precision floating-point ball arithmetic") | |
427 | (description | |
428 | "Arb is a C library for arbitrary-precision floating-point ball | |
6b8e8285 AE |
429 | arithmetic. It supports efficient high-precision computation with |
430 | polynomials, power series, matrices and special functions over the | |
431 | real and complex numbers, with automatic, rigorous error control.") | |
6aa54e23 RW |
432 | (license license:lgpl2.1+) |
433 | (home-page "http://fredrikj.net/arb/"))) | |
6b8e8285 | 434 | |
1d6589db AE |
435 | (define-public python-flint |
436 | (package | |
437 | (name "python-flint") | |
438 | (version "0.3.0") | |
439 | (source (origin | |
440 | (method git-fetch) | |
441 | (uri (git-reference | |
442 | (url "https://github.com/fredrik-johansson/python-flint.git") | |
443 | (commit version))) | |
444 | (file-name (git-file-name name version)) | |
445 | (sha256 | |
446 | (base32 | |
447 | "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw")) | |
448 | (patches (search-patches "python-flint-includes.patch")))) | |
449 | (build-system python-build-system) | |
450 | (native-inputs | |
451 | `(("python-cython" ,python-cython))) | |
452 | (propagated-inputs | |
453 | `(("python-numpy" ,python-numpy))) | |
454 | (inputs | |
455 | `(("arb" ,arb) | |
456 | ("flint" ,flint))) | |
457 | (synopsis "Python module wrapping ARB and FLINT") | |
458 | (description | |
459 | "Python-flint is a Python extension module wrapping FLINT | |
460 | (Fast Library for Number Theory) and Arb (arbitrary-precision ball | |
461 | arithmetic). It supports integers, rationals, modular integers, | |
462 | real and complex ball arithmetic, polynomials and matrices over all | |
463 | these types and other mathematical functions.") | |
464 | (license license:expat) | |
465 | (home-page "http://fredrikj.net/python-flint/"))) | |
466 | ||
14e6520e AE |
467 | (define-public ntl |
468 | (package | |
469 | (name "ntl") | |
470 | (version "9.7.0") | |
471 | (source (origin | |
472 | (method url-fetch) | |
473 | (uri (string-append "http://shoup.net/ntl/ntl-" | |
474 | version ".tar.gz")) | |
475 | (sha256 (base32 | |
476 | "115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq")))) | |
477 | (build-system gnu-build-system) | |
478 | (native-inputs | |
479 | `(("libtool" ,libtool) | |
480 | ("perl" ,perl))) ; for configuration | |
481 | ;; FIXME: Add optional input gf2x once available; then also add | |
482 | ;; configure flag "NTL_GF2X_LIB=on". | |
483 | (inputs | |
484 | `(("gmp" ,gmp))) | |
485 | (arguments | |
486 | `(#:phases | |
487 | (modify-phases %standard-phases | |
488 | (replace 'configure | |
489 | (lambda* (#:key outputs #:allow-other-keys) | |
490 | (chdir "src") | |
491 | (system* "./configure" | |
492 | (string-append "PREFIX=" (assoc-ref outputs "out")) | |
493 | ;; Do not build especially for the build machine. | |
494 | "NATIVE=off" | |
495 | ;; Also do not tune to the build machine. | |
496 | "WIZARD=off" | |
497 | "SHARED=on") | |
498 | #t))))) | |
499 | (synopsis "C++ library for number theory") | |
500 | (description | |
501 | "NTL is a C++ library providing data structures and algorithms | |
502 | for manipulating signed, arbitrary length integers, and for vectors, | |
503 | matrices, and polynomials over the integers and over finite fields.") | |
504 | (license license:gpl2+) | |
505 | (home-page "http://shoup.net/ntl/"))) | |
506 | ||
aae03c48 AE |
507 | (define-public singular |
508 | (package | |
509 | (name "singular") | |
ff6807dc | 510 | (version "4.1.2p1") |
f35c3bbb KK |
511 | (source |
512 | (origin | |
513 | (method url-fetch) | |
514 | (uri | |
515 | (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/" | |
516 | "Singular/SOURCES/" | |
517 | (string-join | |
518 | (string-split | |
519 | (string-trim-right version #\p | |
520 | 0 (1- (string-length version))) | |
521 | #\.) "-") | |
522 | "/singular-" version ".tar.gz")) | |
523 | (sha256 (base32 | |
ff6807dc | 524 | "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m")))) |
aae03c48 AE |
525 | (build-system gnu-build-system) |
526 | (native-inputs | |
527 | `(("doxygen" ,doxygen) | |
528 | ("graphviz" ,graphviz) | |
529 | ("perl" ,perl))) | |
530 | (inputs | |
531 | `(("cddlib" ,cddlib) | |
532 | ("gmp" ,gmp) | |
533 | ("flint" ,flint) | |
534 | ("mpfr" ,mpfr) | |
535 | ("ntl" ,ntl) | |
536 | ("python" ,python-2) | |
537 | ("readline" ,readline))) | |
538 | (arguments | |
539 | `(#:configure-flags | |
540 | (list (string-append "--with-ntl=" | |
541 | (assoc-ref %build-inputs "ntl"))))) | |
542 | (synopsis "Computer algebra system for polynomial computations") | |
543 | (description | |
544 | "Singular is a computer algebra system for polynomial computations, | |
545 | with special emphasis on commutative and non-commutative algebra, algebraic | |
546 | geometry and singularity theory.") | |
547 | ;; Singular itself is dual licensed gpl2 or gpl3, but some of the | |
548 | ;; libraries with which it links are licensed under lgpl3+, so the | |
549 | ;; combined work becomes gpl3. See COPYING in the source code. | |
550 | (license license:gpl3) | |
551 | (home-page "http://www.singular.uni-kl.de/index.php"))) | |
552 | ||
57c9c349 AE |
553 | (define-public gmp-ecm |
554 | (package | |
555 | (name "gmp-ecm") | |
7d15cf17 | 556 | (version "7.0.4") |
57c9c349 | 557 | (source (origin |
7d15cf17 TGR |
558 | (method url-fetch) |
559 | ;; Use the ‘Latest version’ link for a stable URI across releases. | |
560 | (uri (string-append "https://gforge.inria.fr/frs/download.php/" | |
561 | "latestfile/160/ecm-" version ".tar.gz")) | |
562 | (sha256 (base32 | |
563 | "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc")))) | |
57c9c349 AE |
564 | (build-system gnu-build-system) |
565 | (inputs | |
566 | `(("gmp" ,gmp))) | |
567 | (arguments | |
568 | `(#:configure-flags '("--enable-shared" | |
569 | ;; Disable specific assembly routines, which depend | |
570 | ;; on the subarchitecture of the build machine, | |
571 | ;; and use gmp instead. | |
572 | "--disable-asm-redc"))) | |
573 | (synopsis "Integer factorization library using the elliptic curve method") | |
574 | (description | |
575 | "GMP-ECM factors integers using the elliptic curve method (ECM) as well | |
576 | as the P-1 and P+1 algorithms. It provides a library and a stand-alone | |
577 | binary.") | |
578 | ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+, | |
579 | ;; so the combined work is under gpl3+. | |
580 | (license license:gpl3+) | |
581 | (home-page "http://ecm.gforge.inria.fr/"))) | |
582 | ||
ed9f9a77 LC |
583 | (define-public bc |
584 | (package | |
585 | (name "bc") | |
f71f29ca | 586 | (version "1.07.1") |
ed9f9a77 LC |
587 | (source (origin |
588 | (method url-fetch) | |
589 | (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz")) | |
590 | (sha256 | |
591 | (base32 | |
f71f29ca | 592 | "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2")))) |
ed9f9a77 | 593 | (build-system gnu-build-system) |
f71f29ca MB |
594 | (native-inputs |
595 | `(("ed" ,ed) | |
596 | ("flex" ,flex) | |
597 | ("texinfo" ,texinfo))) | |
ed9f9a77 | 598 | (arguments |
f71f29ca | 599 | '(#:configure-flags |
f0bacad6 | 600 | (list "--with-readline"))) |
6fd52309 | 601 | (home-page "https://www.gnu.org/software/bc/") |
f50d2669 | 602 | (synopsis "Arbitrary precision numeric processing language") |
ed9f9a77 | 603 | (description |
a22dc0c4 LC |
604 | "bc is an arbitrary precision numeric processing language. It includes |
605 | an interactive environment for evaluating mathematical statements. Its | |
606 | syntax is similar to that of C, so basic usage is familiar. It also includes | |
607 | \"dc\", a reverse-polish calculator.") | |
9f51293c | 608 | (license license:gpl2+))) |
37e6cdcd | 609 | |
2a9b10c7 RW |
610 | ;; The original kiss-fft does not have a complete build system and does not |
611 | ;; build any shared libraries. This is a fork used by Extempore. | |
612 | (define-public kiss-fft-for-extempore | |
613 | (package | |
614 | (name "kiss-fft-for-extempore") | |
615 | (version "1.3.0") | |
616 | (source (origin | |
9774fac4 RW |
617 | (method git-fetch) |
618 | (uri (git-reference | |
619 | (url "https://github.com/extemporelang/kiss_fft.git") | |
620 | (commit version))) | |
621 | (file-name (git-file-name name version)) | |
2a9b10c7 RW |
622 | (sha256 |
623 | (base32 | |
9774fac4 | 624 | "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2")))) |
2a9b10c7 RW |
625 | (build-system cmake-build-system) |
626 | (arguments `(#:tests? #f)) ; no tests included | |
39162ee4 RW |
627 | ;; Extempore refuses to build on architectures other than x86_64 |
628 | (supported-systems '("x86_64-linux")) | |
2a9b10c7 RW |
629 | (home-page "https://github.com/extemporelang/kiss_fft") |
630 | (synopsis "Mixed-radix Fast Fourier Transform") | |
631 | (description | |
632 | "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT | |
633 | that can use fixed or floating data types and can easily be incorporated into | |
634 | a C program.") | |
635 | (license license:bsd-3))) | |
636 | ||
37e6cdcd LC |
637 | (define-public fftw |
638 | (package | |
639 | (name "fftw") | |
bdb74478 | 640 | (version "3.3.8") |
37e6cdcd LC |
641 | (source (origin |
642 | (method url-fetch) | |
643 | (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-" | |
644 | version".tar.gz")) | |
645 | (sha256 | |
646 | (base32 | |
bdb74478 | 647 | "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1")))) |
37e6cdcd LC |
648 | (build-system gnu-build-system) |
649 | (arguments | |
65bb2279 | 650 | `(#:configure-flags |
69d5909e MW |
651 | '("--enable-shared" "--enable-openmp" "--enable-threads" |
652 | ,@(let ((system (or (%current-target-system) (%current-system)))) | |
653 | ;; Enable SIMD extensions for codelets. See details at: | |
654 | ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>. | |
655 | (cond | |
656 | ((string-prefix? "x86_64" system) | |
657 | '("--enable-sse2" "--enable-avx" "--enable-avx2" | |
658 | "--enable-avx512" "--enable-avx-128-fma")) | |
659 | ((string-prefix? "i686" system) | |
660 | '("--enable-sse2")) | |
661 | ((string-prefix? "aarch64" system) | |
662 | ;; Note that fftw supports NEON on 32-bit ARM only when | |
663 | ;; compiled for single-precision. | |
664 | '("--enable-neon")) | |
665 | (else | |
666 | '()))) | |
65bb2279 EB |
667 | ;; By default '-mtune=native' is used. However, that may cause the |
668 | ;; use of ISA extensions (e.g. AVX) that are not necessarily | |
669 | ;; available on the user's machine when that package is built on a | |
670 | ;; different machine. | |
671 | "ax_cv_c_flags__mtune_native=no"))) | |
37e6cdcd LC |
672 | (native-inputs `(("perl" ,perl))) |
673 | (home-page "http://fftw.org") | |
674 | (synopsis "Computing the discrete Fourier transform") | |
675 | (description | |
676 | "FFTW is a C subroutine library for computing the discrete Fourier | |
677 | transform (DFT) in one or more dimensions, of arbitrary input size, and of | |
678 | both real and complex data (as well as of even/odd data---i.e. the discrete | |
679 | cosine/ sine transforms or DCT/DST).") | |
9f51293c | 680 | (license license:gpl2+))) |
7569c5cb EB |
681 | |
682 | (define-public fftwf | |
683 | (package (inherit fftw) | |
684 | (name "fftwf") | |
685 | (arguments | |
686 | (substitute-keyword-arguments (package-arguments fftw) | |
69d5909e MW |
687 | ((#:configure-flags fftw-configure-flags) |
688 | `(cons* "--enable-single" | |
689 | ,@(if (string-prefix? "arm" (or (%current-target-system) | |
690 | (%current-system))) | |
691 | ;; fftw supports NEON on 32-bit ARM only when compiled | |
692 | ;; for single-precision, so add it here. | |
693 | '("--enable-neon") | |
694 | '()) | |
695 | ,fftw-configure-flags)))) | |
7569c5cb EB |
696 | (description |
697 | (string-append (package-description fftw) | |
698 | " Single-precision version.")))) | |
e5c66f8c EB |
699 | |
700 | (define-public fftw-openmpi | |
701 | (package (inherit fftw) | |
702 | (name "fftw-openmpi") | |
703 | (inputs | |
704 | `(("openmpi" ,openmpi) | |
705 | ,@(package-inputs fftw))) | |
706 | (arguments | |
707 | (substitute-keyword-arguments (package-arguments fftw) | |
708 | ((#:configure-flags cf) | |
eb6785cf EB |
709 | `(cons "--enable-mpi" ,cf)) |
710 | ((#:phases phases '%standard-phases) | |
711 | `(modify-phases ,phases | |
712 | (add-before 'check 'mpi-setup | |
713 | ,%openmpi-setup))))) | |
e5c66f8c EB |
714 | (description |
715 | (string-append (package-description fftw) | |
716 | " With OpenMPI parallelism support.")))) | |
8f4b1dfb | 717 | |
c8d99608 RW |
718 | (define-public java-la4j |
719 | (package | |
720 | (name "java-la4j") | |
721 | (version "0.6.0") | |
722 | (source (origin | |
723 | (method git-fetch) | |
724 | (uri (git-reference | |
725 | (url "https://github.com/vkostyukov/la4j.git") | |
726 | (commit version))) | |
727 | (file-name (string-append name "-" version "-checkout")) | |
728 | (sha256 | |
729 | (base32 | |
730 | "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3")))) | |
731 | (build-system ant-build-system) | |
732 | (arguments | |
733 | `(#:jar-name "la4j.jar" | |
734 | #:jdk ,icedtea-8 | |
735 | #:test-exclude (list "**/Abstract*.java" | |
736 | "**/MatrixTest.java" | |
737 | "**/DenseMatrixTest.java" | |
738 | "**/SparseMatrixTest.java" | |
739 | "**/VectorTest.java" | |
740 | "**/SparseVectorTest.java" | |
741 | "**/DenseVectorTest.java"))) | |
742 | (native-inputs | |
743 | `(("java-junit" ,java-junit) | |
744 | ("java-hamcrest-core" ,java-hamcrest-core))) | |
745 | (home-page "http://la4j.org/") | |
746 | (synopsis "Java library that provides Linear Algebra primitives and algorithms") | |
747 | (description "The la4j library is a Java library that provides Linear | |
748 | Algebra primitives (matrices and vectors) and algorithms. The key features of | |
749 | the la4j library are: | |
750 | ||
751 | @itemize | |
752 | @item No dependencies and tiny size | |
753 | @item Fluent object-oriented/functional API | |
754 | @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices | |
755 | @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other) | |
756 | @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other) | |
757 | @item MatrixMarket/CSV IO formats support for matrices and vectors | |
758 | @end itemize\n") | |
759 | (license license:asl2.0))) | |
760 | ||
24074b0b RW |
761 | (define-public java-jlargearrays |
762 | (package | |
763 | (name "java-jlargearrays") | |
764 | (version "1.6") | |
765 | (source (origin | |
766 | (method url-fetch) | |
767 | (uri (string-append "http://search.maven.org/remotecontent?" | |
768 | "filepath=pl/edu/icm/JLargeArrays/" | |
769 | version "/JLargeArrays-" version | |
770 | "-sources.jar")) | |
771 | (file-name (string-append name "-" version ".jar")) | |
772 | (sha256 | |
773 | (base32 | |
774 | "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a")))) | |
775 | (build-system ant-build-system) | |
776 | (arguments | |
777 | `(#:jar-name "jlargearrays.jar" | |
778 | #:tests? #f ; tests are not included in the release archive | |
779 | #:jdk ,icedtea-8)) | |
780 | (propagated-inputs | |
781 | `(("java-commons-math3" ,java-commons-math3))) | |
782 | (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays") | |
783 | (synopsis "Library of one-dimensional arrays that can store up to 263 elements") | |
784 | (description "JLargeArrays is a Java library of one-dimensional arrays | |
785 | that can store up to 263 elements.") | |
786 | (license license:bsd-2))) | |
787 | ||
4e92911c RW |
788 | (define-public java-jtransforms |
789 | (package | |
790 | (name "java-jtransforms") | |
791 | (version "3.1") | |
792 | (source (origin | |
793 | (method url-fetch) | |
794 | (uri (string-append "http://search.maven.org/remotecontent?" | |
795 | "filepath=com/github/wendykierp/JTransforms/" | |
796 | version "/JTransforms-" version "-sources.jar")) | |
797 | (sha256 | |
798 | (base32 | |
799 | "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg")))) | |
800 | (build-system ant-build-system) | |
801 | (arguments | |
802 | `(#:jar-name "jtransforms.jar" | |
803 | #:tests? #f ; tests are not included in the release archive | |
804 | #:jdk ,icedtea-8)) | |
805 | (propagated-inputs | |
806 | `(("java-commons-math3" ,java-commons-math3) | |
807 | ("java-jlargearrays" ,java-jlargearrays))) | |
808 | (home-page "https://github.com/wendykierp/JTransforms") | |
809 | (synopsis "Multithreaded FFT library written in pure Java") | |
810 | (description "JTransforms is a multithreaded FFT library written in pure | |
811 | Java. Currently, four types of transforms are available: @dfn{Discrete | |
812 | Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete | |
813 | Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).") | |
814 | (license license:bsd-2))) | |
815 | ||
8f4b1dfb LC |
816 | (define-public eigen |
817 | (package | |
818 | (name "eigen") | |
8cd80a4b | 819 | (version "3.3.5") |
8f4b1dfb LC |
820 | (source (origin |
821 | (method url-fetch) | |
822 | (uri (string-append "https://bitbucket.org/eigen/eigen/get/" | |
9b268f12 | 823 | version ".tar.bz2")) |
8f4b1dfb LC |
824 | (sha256 |
825 | (base32 | |
8cd80a4b | 826 | "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk")) |
2abcc935 | 827 | (file-name (string-append name "-" version ".tar.bz2")) |
8f4b1dfb LC |
828 | (modules '((guix build utils))) |
829 | (snippet | |
830 | ;; There are 3 test failures in the "unsupported" directory, | |
831 | ;; but maintainers say it's a known issue and it's unsupported | |
832 | ;; anyway, so just skip them. | |
1137d85b | 833 | '(begin |
44884a9d RW |
834 | (substitute* "unsupported/CMakeLists.txt" |
835 | (("add_subdirectory\\(test.*") | |
836 | "# Do not build the tests for unsupported features.\n")) | |
6cbee49d | 837 | #t)))) |
8f4b1dfb LC |
838 | (build-system cmake-build-system) |
839 | (arguments | |
840 | '(;; Turn off debugging symbols to save space. | |
841 | #:build-type "Release" | |
842 | ||
354f4fe2 | 843 | #:phases (modify-phases %standard-phases |
ef8742ea | 844 | (replace 'check |
354f4fe2 | 845 | (lambda _ |
354f4fe2 LC |
846 | (let* ((cores (parallel-job-count)) |
847 | (dash-j (format #f "-j~a" cores))) | |
1137d85b | 848 | (setenv "EIGEN_SEED" "1") ;for reproducibility |
ef8742ea LC |
849 | ;; First build the tests, in parallel. See |
850 | ;; <http://eigen.tuxfamily.org/index.php?title=Tests>. | |
fbe9c80f | 851 | (invoke "make" "buildtests" dash-j) |
8f4b1dfb | 852 | |
fbe9c80f TGR |
853 | ;; Then run 'CTest' with -V so we get more |
854 | ;; details upon failure. | |
855 | (invoke "ctest" "-V" dash-j))))))) | |
eeb8b0e6 | 856 | (home-page "https://eigen.tuxfamily.org") |
8f4b1dfb LC |
857 | (synopsis "C++ template library for linear algebra") |
858 | (description | |
859 | "Eigen is a C++ template library for linear algebra: matrices, vectors, | |
860 | numerical solvers, and related algorithms. It provides an elegant API based | |
861 | on \"expression templates\". It is versatile: it supports all matrix sizes, | |
862 | all standard numeric types, various matrix decompositions and geometry | |
863 | features, and more.") | |
864 | ||
865 | ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3. | |
866 | ;; See 'COPYING.README' for details. | |
9f51293c | 867 | (license license:mpl2.0))) |
70770b93 | 868 | |
697eb65d RW |
869 | (define-public eigen-for-tensorflow |
870 | (let ((changeset "fd6845384b86") | |
871 | (revision "1")) | |
872 | (package (inherit eigen) | |
873 | (name "eigen-for-tensorflow") | |
874 | (version (string-append "3.3.5-" revision "." changeset)) | |
875 | (source (origin | |
876 | (method hg-fetch) | |
877 | (uri (hg-reference | |
878 | (url "https://bitbucket.org/eigen/eigen") | |
879 | (changeset changeset))) | |
880 | (sha256 | |
881 | (base32 | |
882 | "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5")) | |
883 | (file-name (string-append name "-" version "-checkout")) | |
884 | (modules '((guix build utils))) | |
885 | (snippet | |
886 | ;; There are 3 test failures in the "unsupported" directory, | |
887 | ;; but maintainers say it's a known issue and it's unsupported | |
888 | ;; anyway, so just skip them. | |
889 | '(begin | |
890 | (substitute* "unsupported/CMakeLists.txt" | |
891 | (("add_subdirectory\\(test.*") | |
892 | "# Do not build the tests for unsupported features.\n")) | |
893 | #t))))))) | |
894 | ||
70770b93 FT |
895 | (define-public xtensor |
896 | (package | |
897 | (name "xtensor") | |
98080807 | 898 | (version "0.20.5") |
70770b93 | 899 | (source (origin |
e1ecaa83 KK |
900 | (method git-fetch) |
901 | (uri (git-reference | |
902 | (url "https://github.com/QuantStack/xtensor.git") | |
903 | (commit version))) | |
70770b93 FT |
904 | (sha256 |
905 | (base32 | |
98080807 | 906 | "0kkc4ar7p2d94jnclmrh46dwv7ldy9lx630vm9gci3pp4hnhbj9f")) |
e1ecaa83 | 907 | (file-name (git-file-name name version)))) |
70770b93 FT |
908 | (build-system cmake-build-system) |
909 | (native-inputs | |
910 | `(("googletest" ,googletest) | |
911 | ("xtl" ,xtl))) | |
912 | (arguments | |
913 | `(#:configure-flags | |
914 | '("-DBUILD_TESTS=ON") | |
915 | #:test-target "xtest")) | |
916 | (home-page "http://quantstack.net/xtensor") | |
917 | (synopsis "C++ tensors with broadcasting and lazy computing") | |
918 | (description "xtensor is a C++ library meant for numerical analysis with | |
919 | multi-dimensional array expressions. | |
920 | ||
921 | xtensor provides: | |
922 | @itemize | |
923 | @item an extensible expression system enabling lazy broadcasting. | |
924 | @item an API following the idioms of the C++ standard library. | |
925 | @item tools to manipulate array expressions and build upon xtensor. | |
926 | @end itemize") | |
927 | (license license:bsd-3))) | |
3f074a21 AE |
928 | |
929 | (define-public gap | |
930 | (package | |
931 | (name "gap") | |
bf95a142 | 932 | (version "4.10.1") |
3f074a21 AE |
933 | (source |
934 | (origin | |
935 | (method url-fetch) | |
936 | (uri (string-append "https://www.gap-system.org/pub/gap/gap-" | |
937 | (version-major+minor version) | |
938 | "/tar.bz2/gap-" | |
939 | version | |
940 | ".tar.bz2")) | |
941 | (sha256 | |
942 | (base32 | |
bf95a142 | 943 | "136s0zvhcw41fshj5zgsrjcy2kd58cdh2m3ddp5rdizi4rx54f10")) |
3f074a21 AE |
944 | (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1))) |
945 | (snippet | |
946 | '(begin | |
947 | ;; Delete the external gmp and zlib libraries | |
948 | ;; and a subdirectory not needed for our build. | |
949 | (for-each delete-file-recursively | |
950 | '("extern" "hpcgap")) | |
951 | ;; Delete a failing test. | |
952 | ;; FIXME: This might be fixed in the next release, see | |
953 | ;; https://github.com/gap-system/gap/issues/3292 | |
954 | (delete-file "tst/testinstall/dir.tst") | |
955 | ;; Delete all packages except for a fixed list. | |
956 | (with-directory-excursion "pkg" | |
957 | (for-each delete-file-recursively | |
958 | (lset-difference string=? (scandir ".") | |
959 | '("." ".." | |
960 | ;; Necessary packages. | |
961 | "GAPDoc-1.6.2" | |
962 | "primgrp-3.3.2" | |
963 | "SmallGrp-1.3" ; artistic2.0 | |
964 | "transgrp" ; artistic2.0 for data, | |
965 | ; gpl2 or gpl3 for code | |
966 | ;; Recommanded package. | |
967 | "io-4.5.4" ; gpl3+ | |
968 | ;; Optional packages, searched for at start, | |
969 | ;; and their depedencies. | |
970 | "alnuth-3.1.0" | |
3f074a21 AE |
971 | "autpgrp-1.10" |
972 | "crisp-1.4.4" ; bsd-2 | |
bf95a142 | 973 | "ctbllib" ; gpl3+ according to doc/chap0.txt |
3f074a21 AE |
974 | "FactInt-1.6.2" |
975 | "fga" | |
976 | "irredsol-1.4" ; bsd-2 | |
bf95a142 | 977 | "laguna-3.9.2" |
3f074a21 AE |
978 | "polenta-1.3.8" |
979 | "polycyclic-2.14" | |
980 | "radiroot-2.8" | |
981 | "resclasses-4.7.1" | |
982 | "sophus-1.24" | |
bf95a142 AE |
983 | "tomlib-1.2.7" ; gpl2+, clarified in the git repository |
984 | ; and the next release | |
3f074a21 AE |
985 | "utils-0.59")))) |
986 | #t)))) | |
987 | (build-system gnu-build-system) | |
988 | (inputs | |
989 | `(("gmp" ,gmp) | |
990 | ("zlib" ,zlib))) | |
991 | (arguments | |
bf95a142 AE |
992 | `(#:modules ((ice-9 ftw) |
993 | (srfi srfi-26) | |
994 | (guix build gnu-build-system) | |
995 | (guix build utils)) | |
996 | #:phases | |
3f074a21 AE |
997 | (modify-phases %standard-phases |
998 | (add-after 'build 'build-packages | |
999 | ;; Compile all packages that have not been deleted by the | |
1000 | ;; code snippet above. | |
1001 | (lambda _ | |
1002 | (setenv "CONFIG_SHELL" (which "bash")) | |
1003 | (with-directory-excursion "pkg" | |
1004 | (invoke "../bin/BuildPackages.sh") | |
1005 | #t))) | |
1006 | (add-after 'build-packages 'build-doc | |
1007 | ;; The documentation is bundled, but we create it from source. | |
1008 | (lambda _ | |
1009 | (with-directory-excursion "doc" | |
1010 | (invoke "./make_doc")) | |
1011 | #t)) | |
3f074a21 AE |
1012 | (replace 'install |
1013 | (lambda* (#:key outputs #:allow-other-keys) | |
1014 | (let* ((out (assoc-ref outputs "out")) | |
1015 | (bin (string-append out "/bin")) | |
bf95a142 | 1016 | (lib (string-append out "/lib")) |
3f074a21 AE |
1017 | (prog (string-append bin "/gap")) |
1018 | (prog-real (string-append bin "/.gap-real")) | |
1019 | (share (string-append out "/share/gap")) | |
bf95a142 AE |
1020 | (include (string-append out "/include/gap")) |
1021 | (include-hpc (string-append include "/hpc"))) | |
3f074a21 AE |
1022 | ;; Install only the gap binary; the gac compiler is left |
1023 | ;; for maybe later. "Wrap" it in a shell script that calls | |
1024 | ;; the binary with the correct parameter. | |
1025 | (mkdir-p bin) | |
1026 | (copy-file "gap" prog-real) | |
1027 | (call-with-output-file prog | |
1028 | (lambda (port) | |
1029 | (format port | |
1030 | "#!~a~%exec ~a -l ~a \"$@\"~%" | |
1031 | (which "bash") | |
1032 | prog-real | |
1033 | share))) | |
1034 | (chmod prog #o755) | |
bf95a142 AE |
1035 | ;; Install the headers, which are needed by Sage. The |
1036 | ;; Makefile target "install-headers" was available in | |
1037 | ;; gap-4.10.0, but has been commented out in gap-4.10.1. | |
1038 | (mkdir-p include-hpc) | |
3f074a21 | 1039 | (install-file "gen/config.h" include) |
bf95a142 AE |
1040 | (let ((file-name-predicate-without-stat |
1041 | (lambda (regex) | |
1042 | (cut (file-name-predicate regex) <> #f)))) | |
1043 | (with-directory-excursion "src" | |
1044 | (for-each | |
1045 | (cut install-file <> include) | |
1046 | (scandir "." | |
1047 | (file-name-predicate-without-stat ".*\\.h$")))) | |
1048 | (with-directory-excursion "src/hpc" | |
1049 | (for-each | |
1050 | (cut install-file <> include-hpc) | |
1051 | (scandir "." | |
1052 | (file-name-predicate-without-stat ".*\\.h$"))))) | |
1053 | ;; Install the library, which is needed by Sage. The | |
1054 | ;; Makefile target "install-libgap" was available in | |
1055 | ;; gap-4.10.0, but has been commented out in gap-4.10.1. | |
1056 | ;; Compared to the Makefile, which used libtool, the | |
1057 | ;; following approach of copying files and making symlinks | |
1058 | ;; is rather pedestrian. There is hope that some later | |
1059 | ;; version of gap reinstates and completes the install | |
1060 | ;; targets. | |
1061 | (invoke "make" "libgap.la") | |
1062 | (install-file "libgap.la" lib) | |
1063 | (install-file ".libs/libgap.so.0.0.0" lib) | |
1064 | (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so")) | |
1065 | (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0")) | |
3f074a21 AE |
1066 | ;; Install a certain number of files and directories to |
1067 | ;; SHARE, where the wrapped shell script expects them. | |
1068 | ;; Remove information on the build directory from sysinfo.gap. | |
1069 | (substitute* "sysinfo.gap" | |
1070 | (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"") | |
1071 | (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"") | |
1072 | (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\"")) | |
1073 | (install-file "sysinfo.gap" share) | |
1074 | (copy-recursively "grp" (string-append share "/grp")) | |
1075 | (copy-recursively "pkg" (string-append share "/pkg")) | |
1076 | ;; The following is not the C library libgap.so, but a | |
1077 | ;; library of GAP code. | |
1078 | (copy-recursively "lib" (string-append share "/lib")) | |
1079 | ;; The gap binary looks for documentation inside SHARE. | |
1080 | (copy-recursively "doc" (string-append share "/doc"))) | |
1081 | #t))))) | |
1082 | (home-page "https://www.gap-system.org/") | |
1083 | (synopsis | |
1084 | "System for computational group theory") | |
1085 | (description | |
1086 | "GAP is a system for computational discrete algebra, with particular | |
1087 | emphasis on computational group theory. It provides a programming language, | |
1088 | a library of thousands of functions implementing algebraic algorithms | |
1089 | written in the GAP language as well as large data libraries of algebraic | |
1090 | objects.") | |
1091 | ;; Some packages have different licenses (effectively forcing the | |
1092 | ;; combined work to be licensed as gpl3+); if this is the case, this | |
1093 | ;; is mentioned above next to their name. | |
1094 | ;; Some packages have no license mentioned explicitly; supposedly this | |
1095 | ;; means that the gpl2+ licence of GAP itself applies, but to be on the | |
1096 | ;; safe side, we drop them for now. | |
1097 | (license license:gpl2+))) | |
f0fbb31d AE |
1098 | |
1099 | (define-public givaro | |
1100 | (package | |
1101 | (name "givaro") | |
1102 | (version "4.1.1") | |
1103 | (source (origin | |
1104 | (method git-fetch) | |
1105 | (uri (git-reference | |
1106 | (url "https://github.com/linbox-team/givaro") | |
1107 | (commit (string-append "v" version)))) | |
1108 | (file-name (git-file-name name version)) | |
1109 | (sha256 | |
1110 | (base32 | |
1111 | "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk")))) | |
1112 | (build-system gnu-build-system) | |
1113 | (native-inputs | |
1114 | `(("autoconf" ,autoconf) | |
1115 | ("automake" ,automake) | |
1116 | ("libtool" ,libtool))) | |
1117 | (propagated-inputs | |
1118 | `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h | |
1119 | (arguments | |
1120 | `(#:phases | |
1121 | (modify-phases %standard-phases | |
1122 | (add-before 'bootstrap 'setenv | |
1123 | ;; Prevent the autogen.sh script to carry out the configure | |
1124 | ;; script, which has not yet been patched to replace /bin/sh. | |
1125 | (lambda _ | |
1126 | (setenv "NOCONFIGURE" "yes") | |
1127 | #t))))) | |
1128 | (synopsis "Algebraic computations with exact rings and fields") | |
1129 | (description | |
1130 | "Givaro is a C++ library implementing the basic arithmetic of various | |
1131 | algebraic objects: prime fields, extension fields, finite fields, finite | |
1132 | rings, polynomials, algebraic numbers, arbitrary precision integers and | |
1133 | rationals (C++ wrappers over gmp), fixed precision integers. It also | |
1134 | provides data-structures and templated classes for the manipulation of | |
1135 | compound objects, such as vectors, matrices and univariate polynomials.") | |
1136 | (license license:cecill-b) | |
1137 | (home-page "https://github.com/linbox-team/givaro"))) | |
4bf9cb40 AE |
1138 | |
1139 | (define-public fflas-ffpack | |
1140 | (package | |
1141 | (name "fflas-ffpack") | |
1142 | (version "2.4.3") | |
1143 | (source (origin | |
1144 | (method git-fetch) | |
1145 | (uri (git-reference | |
1146 | (url "https://github.com/linbox-team/fflas-ffpack") | |
1147 | (commit version))) | |
1148 | (file-name (git-file-name name version)) | |
1149 | (sha256 | |
1150 | (base32 | |
1151 | "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74")))) | |
1152 | (build-system gnu-build-system) | |
1153 | (native-inputs | |
1154 | `(("autoconf" ,autoconf) | |
1155 | ("automake" ,automake) | |
1156 | ("libtool" ,libtool) | |
1157 | ("pkg-config" ,pkg-config))) | |
1158 | (inputs | |
1159 | `(("openblas" ,openblas))) | |
1160 | (propagated-inputs | |
1161 | `(("givaro" ,givaro))) ; required according to the .pc file | |
1162 | (arguments | |
1163 | `(#:configure-flags | |
1164 | (list (string-append "--with-blas-libs=" | |
1165 | (assoc-ref %build-inputs "openblas") | |
1166 | "/lib/libopenblas.so")) | |
1167 | #:phases | |
1168 | (modify-phases %standard-phases | |
1169 | (add-before 'bootstrap 'setenv | |
1170 | ;; Prevent the autogen.sh script to carry out the configure | |
1171 | ;; script, which has not yet been patched to replace /bin/sh. | |
1172 | (lambda _ | |
1173 | (setenv "NOCONFIGURE" "yes") | |
1174 | #t))))) | |
1175 | (synopsis "C++ library for linear algebra over finite fields") | |
1176 | (description | |
1177 | "FFLAS-FFPACK is a C++ template library for basic linear algebra | |
1178 | operations over a finite field. | |
1179 | FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation | |
1180 | of a subset of routines of the numerical BLAS; it also supports sparse | |
1181 | matrix-vector products. | |
1182 | FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK | |
1183 | library to provide functionalities of higher level, using the kernel | |
1184 | of a BLAS. Additionally, it provides routines specific to exact linear | |
1185 | algebra, such as the row echelon form.") | |
1186 | (license license:lgpl2.1+) | |
1187 | (home-page "https://linbox-team.github.io/fflas-ffpack/"))) | |
a612f866 AE |
1188 | |
1189 | (define-public linbox | |
1190 | (package | |
1191 | (name "linbox") | |
1192 | (version "1.6.3") | |
1193 | (source (origin | |
1194 | (method git-fetch) | |
1195 | (uri (git-reference | |
1196 | (url "https://github.com/linbox-team/linbox") | |
1197 | (commit (string-append "v" version)))) | |
1198 | (file-name (git-file-name name version)) | |
1199 | (sha256 | |
1200 | (base32 | |
1201 | "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571")))) | |
1202 | (build-system gnu-build-system) | |
1203 | (native-inputs | |
1204 | `(("autoconf" ,autoconf) | |
1205 | ("automake" ,automake) | |
1206 | ("libtool" ,libtool) | |
1207 | ("pkg-config" ,pkg-config))) | |
1208 | (inputs | |
1209 | `(("fflas-ffpack" ,fflas-ffpack))) | |
1210 | (arguments | |
1211 | `(#:phases | |
1212 | (modify-phases %standard-phases | |
1213 | (add-before 'bootstrap 'setenv | |
1214 | ;; Prevent the autogen.sh script to carry out the configure | |
1215 | ;; script, which has not yet been patched to replace /bin/sh. | |
1216 | (lambda _ | |
1217 | (setenv "NOCONFIGURE" "yes") | |
1218 | #t))))) | |
1219 | (synopsis "C++ library for linear algebra over exact rings") | |
1220 | (description | |
1221 | "LinBox is a C++ template library for exact linear algebra computation | |
1222 | with dense, sparse, and structured matrices over the integers and over | |
1223 | finite fields.") | |
1224 | (license license:lgpl2.1+) | |
1225 | (home-page "https://linbox-team.github.io/linbox/"))) |