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Revert "gnu: maxima: Ensure gcc is available at runtime."
[jackhill/guix/guix.git] / gnu / packages / maths.scm
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8f8b2451 1;;; GNU Guix --- Functional package management for GNU
b146763a 2;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
da95c817 3;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
a53d6719 4;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
dfdf5716 5;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
df354a77 6;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
182d6311 7;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
612a387f 8;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
32158110 9;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
9aafbc0c 10;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
83a34647 11;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
45147b0c 12;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
ec8c7e47 13;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
b7b27a8f 14;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
5d4bd4cc 15;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
d7cff656 16;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
0f43f835 17;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
5d4bd4cc 18;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
54052a54 19;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
ba1be533 20;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
8f8b2451
AE		 21;;;
22;;; This file is part of GNU Guix.
23;;;
24;;; GNU Guix is free software; you can redistribute it and/or modify it
25;;; under the terms of the GNU General Public License as published by
26;;; the Free Software Foundation; either version 3 of the License, or (at
27;;; your option) any later version.
28;;;
29;;; GNU Guix is distributed in the hope that it will be useful, but
30;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32;;; GNU General Public License for more details.
33;;;
34;;; You should have received a copy of the GNU General Public License
35;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
36
37(define-module (gnu packages maths)
ec322be2 38 #:use-module (ice-9 regex)
8f8b2451 39 #:use-module (gnu packages)
b5b73a82 40 #:use-module ((guix licenses) #:prefix license:)
8f8b2451
AE		 41 #:use-module (guix packages)
42 #:use-module (guix download)
54052a54 43 #:use-module (guix git-download)
0e2672ae 44 #:use-module (guix utils)
cec86422 45 #:use-module (guix build utils)
da95c817 46 #:use-module (guix build-system cmake)
c9dfa3c7 47 #:use-module (guix build-system gnu)
ba1be533 48 #:use-module (guix build-system ocaml)
ec8c7e47 49 #:use-module (guix build-system r)
3de01d3f 50 #:use-module (gnu packages algebra)
5143517c 51 #:use-module (gnu packages autotools)
3de01d3f 52 #:use-module (gnu packages bison)
a17d4564 53 #:use-module (gnu packages boost)
e73b49fb 54 #:use-module (gnu packages check)
3de01d3f 55 #:use-module (gnu packages cmake)
c9dfa3c7 56 #:use-module (gnu packages compression)
668c06ac 57 #:use-module (gnu packages curl)
b7b27a8f 58 #:use-module (gnu packages cyrus-sasl)
528bb464 59 #:use-module (gnu packages documentation)
57e544e8 60 #:use-module (gnu packages elf)
3de01d3f 61 #:use-module (gnu packages flex)
668c06ac 62 #:use-module (gnu packages fltk)
f3929800 63 #:use-module (gnu packages fontutils)
1dba6407 64 #:use-module (gnu packages gettext)
da95c817 65 #:use-module (gnu packages gcc)
73fed4f8 66 #:use-module (gnu packages gd)
668c06ac 67 #:use-module (gnu packages ghostscript)
889187a4 68 #:use-module (gnu packages graphviz)
f3929800 69 #:use-module (gnu packages gtk)
45147b0c 70 #:use-module (gnu packages image)
668c06ac 71 #:use-module (gnu packages less)
8731e527 72 #:use-module (gnu packages lisp)
bc3a2e35 73 #:use-module (gnu packages logging)
6e64766a 74 #:use-module (gnu packages lua)
5698b8b8 75 #:use-module (gnu packages gnome)
1b39a196 76 #:use-module (gnu packages guile)
668c06ac
JD		 77 #:use-module (gnu packages xorg)
78 #:use-module (gnu packages gl)
9f913401 79 #:use-module (gnu packages imagemagick)
8731e527 80 #:use-module (gnu packages m4)
d8c7eeb9 81 #:use-module (gnu packages mpi)
b92eee75 82 #:use-module (gnu packages multiprecision)
528bb464 83 #:use-module (gnu packages netpbm)
ba1be533 84 #:use-module (gnu packages ocaml)
668c06ac 85 #:use-module (gnu packages pcre)
5698b8b8 86 #:use-module (gnu packages popt)
c9dfa3c7
AE		 87 #:use-module (gnu packages perl)
88 #:use-module (gnu packages pkg-config)
da95c817 89 #:use-module (gnu packages python)
c9dfa3c7 90 #:use-module (gnu packages readline)
2742f87e 91 #:use-module (gnu packages tbb)
479c4273 92 #:use-module (gnu packages scheme)
b7194849 93 #:use-module (gnu packages shells)
df354a77 94 #:use-module (gnu packages tcl)
668c06ac 95 #:use-module (gnu packages texinfo)
8f9ac901 96 #:use-module (gnu packages tex)
b7b27a8f 97 #:use-module (gnu packages tls)
9aafbc0c 98 #:use-module (gnu packages wxwidgets)
c12efc72 99 #:use-module (gnu packages xml)
a17d4564 100 #:use-module (srfi srfi-1))
8f8b2451 101
193abc82
JD		 102(define-public aris
103 (package
1f45f18a
JD		 104 (name "aris")
105 (version "2.2")
106 (source (origin
107 (method url-fetch)
108 (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
109 (sha256 (base32
110 "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
111 (build-system gnu-build-system)
112 (inputs `(("gtk+" ,gtk+)
113 ("libxml2" ,libxml2)))
114 (native-inputs `(("pkg-config" ,pkg-config)))
115 (synopsis "Natural deduction first-order logic interface")
116 (description "Aris is a program for performing logical proofs. It supports
117propositional and predicate logic, as well as Boolean algebra and
118arithmetical logic. In addition to its predefined inference and equivalence
119rules, Aris also supports references to older proofs. Its use of standard
120logical symbols and its natural deduction interface make it easy to use for
121beginners.")
122 (license license:gpl3+)
6fd52309 123 (home-page "https://www.gnu.org/software/aris/")))
193abc82 124
9c45c519
JD		 125(define-public c-graph
126 (package
127 (name "c-graph")
128 (version "2.0")
129 (source (origin
130 (method url-fetch)
131 (uri (string-append "mirror://gnu/c-graph/c-graph-" version
132 ".tar.gz"))
133 (sha256 (base32
134 "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
135 (build-system gnu-build-system)
136 (inputs
137 `(("fortran" ,gfortran)))
a3947cb1 138 (synopsis "Visualizing and demonstrating convolution")
9c45c519 139 (description
a3947cb1
LC		 140 "GNU C-Graph is a tool for demonstrating the theory of convolution.
141Thus, it can serve as an excellent aid to students of signal and systems
142theory in visualizing the convolution process. Rather than forcing the
143student to write code, the program offers an intuitive interface with
144interactive dialogs to guide them.")
9c45c519 145 (license license:gpl3+)
6fd52309 146 (home-page "https://www.gnu.org/software/c-graph/")))
9c45c519 147
d91025e3
TD		 148(define-public coda
149 (package
150 (name "coda")
cbfbcb21 151 (version "2.18")
d91025e3
TD		 152 (source
153 (origin
154 (method url-fetch)
155 (uri (string-append "https://github.com/stcorp/coda/releases/download/"
156 version "/coda-" version ".tar.gz"))
157 (sha256
cbfbcb21 158 (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs"))
4b12fe5c
TD		 159 (patches (search-patches "coda-use-system-libs.patch"))
160 (modules '((guix build utils)))
161 (snippet
162 ;; Make sure we don't use the bundled software.
163 '(for-each (lambda (d)
164 (delete-file-recursively (string-append "libcoda/" d)))
165 '("zlib" "pcre" "expat")))))
d91025e3
TD		 166 (native-inputs
167 `(("fortran" ,gfortran)
168 ("python" ,python)
169 ("python-numpy" ,python-numpy)))
170 (inputs
171 `(("zlib" ,zlib)
4b12fe5c
TD		 172 ("pcre" ,pcre)
173 ("expat" ,expat)
d91025e3
TD		 174 ("hdf4" ,hdf4-alt)
175 ("hdf5" ,hdf5)))
176 (build-system gnu-build-system)
177 (arguments
4b12fe5c
TD		 178 '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
179 "LIBS= -lz -lpcre -lexpat")))
d91025e3
TD		 180 (synopsis "A common interface to various earth observation data formats")
181 (description
182 "The Common Data Access toolbox (CODA) provides a set of interfaces for
183reading remote sensing data from earth observation data files. It consists of
184command line applications and interfaces to the C, Fortran, Python, and Java
185programming languages.")
186 (home-page "https://stcorp.nl/coda")
187 (license license:gpl2+)))
188
8f8b2451
AE		 189(define-public units
190 (package
191 (name "units")
cf8d0687 192 (version "2.14")
8f8b2451
AE		 193 (source (origin
194 (method url-fetch)
195 (uri (string-append "mirror://gnu/units/units-" version
196 ".tar.gz"))
197 (sha256 (base32
cf8d0687 198 "1s421bxm36akjsy3qzg6da1d1g20gh094ac2slqxipgkh8yqjcwx"))))
8f8b2451
AE		 199 (build-system gnu-build-system)
200 (synopsis "Conversion between thousands of scales")
201 (description
574e86f9 202 "GNU Units converts numeric quantities between units of measure. It
7c125ce0
AK		 203can handle scale changes through adaptive usage of standard scale
204prefixes (micro-, kilo-, etc.). It can also handle nonlinear
205conversions such as Fahrenheit to Celsius. Its interpreter is powerful
206enough to be used effectively as a scientific calculator.")
8f8b2451 207 (license license:gpl3+)
6fd52309 208 (home-page "https://www.gnu.org/software/units/")))
c9dfa3c7 209
61a529b4
RW		 210(define-public double-conversion
211 (package
212 (name "double-conversion")
213 (version "1.1.5")
214 (source (origin
215 (method url-fetch)
216 (uri (string-append
217 "https://github.com/floitsch/double-conversion/archive/v"
218 version ".tar.gz"))
219 (file-name (string-append name "-" version ".tar.gz"))
220 (sha256
221 (base32
222 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
223 (build-system cmake-build-system)
224 (arguments
225 '(#:test-target "test"
226 #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
227 "-DBUILD_TESTING=ON")))
228 (home-page "https://github.com/floitsch/double-conversion")
229 (synopsis "Conversion routines for IEEE doubles")
230 (description
231 "The double-conversion library provides binary-decimal and decimal-binary
232routines for IEEE doubles. The library consists of efficient conversion
233routines that have been extracted from the V8 JavaScript engine.")
234 (license license:bsd-3)))
235
182d6311
ML		 236(define-public dionysus
237 (package
238 (name "dionysus")
239 (version "1.3.0")
240 (source (origin
241 (method url-fetch)
242 (uri (string-append "mirror://gnu/dionysus/dionysus-" version
243 ".tar.gz"))
244 (sha256
245 (base32
246 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
247 (build-system gnu-build-system)
248 (inputs `(("tcl" ,tcl))) ;for 'tclsh'
249 (synopsis "Local search for universal constants and scientific values")
250 (description
251 "GNU Dionysus is a convenient system for quickly retrieving the values of
252mathematical constants used in science and engineering. Values can be
253searched using a simple command-line tool, choosing from three databases:
254universal constants, atomic numbers, and constants related to
255semiconductors.")
256 (license license:gpl3+)
6fd52309 257 (home-page "https://www.gnu.org/software/dionysus/")))
182d6311 258
88bd1804
AE		 259(define-public gsl
260 (package
261 (name "gsl")
f885fc05 262 (version "2.4")
ab2cc5cd
LC		 263 (source (origin
264 (method url-fetch)
265 (uri (string-append "mirror://gnu/gsl/gsl-"
266 version ".tar.gz"))
267 (sha256
268 (base32
f885fc05 269 "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd"))
ab2cc5cd 270 (patches (search-patches "gsl-test-i686.patch"))))
88bd1804 271 (build-system gnu-build-system)
71e0f288 272 (arguments
f885fc05 273 `(;; Currently there are numerous tests that fail on "exotic"
6f766069
EF		 274 ;; architectures such as aarch64 and ppc64le.
275 ,@(if (string-prefix? "aarch64-linux"
276 (or (%current-target-system) (%current-system)))
277 '(#:tests? #f)
278 '())))
279 (home-page "https://www.gnu.org/software/gsl/")
88bd1804
AE		 280 (synopsis "Numerical library for C and C++")
281 (description
a22dc0c4
LC		 282 "The GNU Scientific Library is a library for numerical analysis in C
283and C++. It includes a wide range of mathematical routines, with over 1000
284functions in total. Subject areas covered by the library include:
285differential equations, linear algebra, Fast Fourier Transforms and random
286numbers.")
88bd1804
AE		 287 (license license:gpl3+)))
288
ba1be533
BW		 289(define-public ocaml-gsl
290 (package
291 (name "ocaml-gsl")
292 (version "1.19.3")
293 (source
294 (origin
295 (method url-fetch)
296 (uri
297 (string-append
298 "https://github.com/mmottl/gsl-ocaml/releases/download/v"
299 version"/gsl-ocaml-" version ".tar.gz"))
300 (sha256
301 (base32
302 "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
303 (build-system ocaml-build-system)
304 (inputs
305 `(("gsl" ,gsl)))
306 (home-page "https://mmottl.github.io/gsl-ocaml")
307 (synopsis "Bindings to the GNU Scientific Library")
308 (description
309 "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
310the OCaml language.")
311 (license license:gpl3+)))
312
7adaab9f
BW		 313(define-public ocaml4.01-gsl
314 (package-with-ocaml4.01 ocaml-gsl))
315
b92eee75
AE		 316(define-public glpk
317 (package
318 (name "glpk")
299b0525 319 (version "4.62")
b92eee75
AE		 320 (source
321 (origin
322 (method url-fetch)
323 (uri (string-append "mirror://gnu/glpk/glpk-"
324 version ".tar.gz"))
325 (sha256
326 (base32
299b0525 327 "0w7s3869ybwyq9a4490dikpib1qp3jnn5nqz1vvwqy1qz3ilnvh9"))))
b92eee75
AE		 328 (build-system gnu-build-system)
329 (inputs
330 `(("gmp" ,gmp)))
331 (arguments
332 `(#:configure-flags '("--with-gmp")))
82110ef6 333 (home-page "https://www.gnu.org/software/glpk/")
79c311b8 334 (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
b92eee75
AE		 335 (description
336 "GLPK is a C library for solving large-scale linear programming (LP),
337mixed integer programming (MIP), and other related problems. It supports the
338GNU MathProg modeling language, a subset of the AMPL language, and features a
339translator for the language. In addition to the C library, a stand-alone
340LP/MIP solver is included in the package.")
341 (license license:gpl3+)))
342
b146763a
AE		 343(define-public 4ti2
344 (package
345 (name "4ti2")
346 (version "1.6.7")
347 (source
348 (origin
349 (method url-fetch)
350 (uri (string-append "http://www.4ti2.de/version_" version
351 "/4ti2-" version ".tar.gz"))
352 (sha256
353 (base32
354 "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
355 (build-system gnu-build-system)
356 (native-inputs
357 `(("which" ,(@ (gnu packages base) which)))) ; for the tests
358 (inputs
359 `(("glpk" ,glpk)
360 ("gmp" ,gmp)))
361 (home-page "http://www.4ti2.de/")
362 (synopsis "Mathematical tool suite for problems on linear spaces")
363 (description
364 "4ti2 implements algorithms for solving algebraic, geometric and
365combinatorial problems on linear spaces. Among others, it solves systems
366of linear equations, computes extreme rays of polyhedral cones, solves
367integer programming problems and computes Markov bases for statistics.")
368 (license license:gpl2+)))
369
53696f10
AE		 370(define-public cddlib
371 (package
372 (name "cddlib")
373 (version "0.94h")
374 (source
375 (origin
376 (method url-fetch)
182dde82 377 (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
53696f10
AE		 378 (string-delete #\. version) ".tar.gz"))
379 (sha256
380 (base32
381 "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
382 (build-system gnu-build-system)
383 (inputs
384 `(("gmp" ,gmp)))
385 (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
386 (synopsis "Library for convex hulls and extreme rays of polyhedra")
387 (description
388 "The C-library cddlib implements the Double Description Method of
389Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
390rays of a general convex polyhedron given by a system of linear inequalities
391in arbitrary dimension. It can also be used for the converse operation of
392computing convex hulls.")
393 (license license:gpl2+)))
394
865a69dd
RW		 395(define-public arpack-ng
396 (package
397 (name "arpack-ng")
398 (version "3.2.0")
399 (source
400 (origin
401 (method url-fetch)
402 (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
403 version ".tar.gz"))
f586c877 404 (file-name (string-append name "-" version ".tar.gz"))
865a69dd
RW		 405 (sha256
406 (base32
407 "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
408 (build-system gnu-build-system)
409 (home-page "https://github.com/opencollab/arpack-ng")
410 (inputs
411 `(("lapack" ,lapack)
19afbea1 412 ("fortran" ,gfortran)))
865a69dd
RW		 413 (synopsis "Fortran subroutines for solving eigenvalue problems")
414 (description
415 "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
416large scale eigenvalue problems.")
166191b3 417 (license (license:non-copyleft "file://COPYING"
865a69dd
RW		 418 "See COPYING in the distribution."))))
419
8c94c886
EB		 420(define-public arpack-ng-openmpi
421 (package (inherit arpack-ng)
422 (name "arpack-ng-openmpi")
423 (inputs
424 `(("mpi" ,openmpi)
425 ,@(package-inputs arpack-ng)))
426 (arguments `(#:configure-flags '("--enable-mpi")))
427 (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
428
da95c817
NK		 429(define-public lapack
430 (package
431 (name "lapack")
ef39a177 432 (version "3.7.1")
da95c817
NK		 433 (source
434 (origin
435 (method url-fetch)
436 (uri (string-append "http://www.netlib.org/lapack/lapack-"
437 version ".tgz"))
438 (sha256
439 (base32
7c0d4c3a 440 "1j51r7n5w4k7r3lrvy7710xrpkg40wf4rqnmngfz6ck9ypckzign"))))
da95c817
NK		 441 (build-system cmake-build-system)
442 (home-page "http://www.netlib.org/lapack/")
19afbea1 443 (inputs `(("fortran" ,gfortran)
da95c817
NK		 444 ("python" ,python-2)))
445 (arguments
3ab869b6
LC		 446 `(#:configure-flags (list
447 ;; Install to PREFIX/lib (the default is
448 ;; PREFIX/lib64).
449 (string-append "-DCMAKE_INSTALL_LIBDIR="
450 (assoc-ref %outputs "out")
451 "/lib")
11f0c4e8 452
3ab869b6
LC		 453 "-DBUILD_SHARED_LIBS:BOOL=YES"
454 "-DLAPACKE=ON"
455
456 ;; Build the 'LAPACKE_clatms' functions.
457 "-DLAPACKE_WITH_TMG=ON")
da95c817 458 #:phases (alist-cons-before
6a995754
LC		 459 'check 'patch-python
460 (lambda* (#:key inputs #:allow-other-keys)
461 (let ((python (assoc-ref inputs "python")))
462 (substitute* "lapack_testing.py"
463 (("/usr/bin/env python") python))))
06ed5982 464 %standard-phases)))
da95c817
NK		 465 (synopsis "Library for numerical linear algebra")
466 (description
467 "LAPACK is a Fortran 90 library for solving the most commonly occurring
468problems in numerical linear algebra.")
166191b3 469 (license (license:non-copyleft "file://LICENSE"
da95c817 470 "See LICENSE in the distribution."))))
73fed4f8 471
e1ff597a
EB		 472(define-public scalapack
473 (package
474 (name "scalapack")
475 (version "2.0.2")
476 (source
477 (origin
478 (method url-fetch)
479 (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
480 version ".tgz"))
481 (sha256
482 (base32
483 "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))))
484 (build-system cmake-build-system)
485 (inputs
486 `(("mpi" ,openmpi)
487 ("fortran" ,gfortran)
488 ("lapack" ,lapack))) ;for testing only
489 (arguments
490 `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")))
491 (home-page "http://www.netlib.org/scalapack/")
492 (synopsis "Library for scalable numerical linear algebra")
493 (description
494 "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
495routines on parallel distributed memory machines. ScaLAPACK solves dense and
496banded linear systems, least squares problems, eigenvalue problems, and
497singular value problems.")
498 (license (license:bsd-style "file://LICENSE"
499 "See LICENSE in the distribution."))))
500
73fed4f8 501(define-public gnuplot
5f800540
KK		 502 (package
503 (name "gnuplot")
7d873e0c 504 (version "5.0.6")
5f800540
KK		 505 (source (origin
506 (method url-fetch)
507 (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
508 version "/gnuplot-"
509 version ".tar.gz"))
510 (sha256
511 (base32
7d873e0c 512 "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv"))))
5f800540
KK		 513 (build-system gnu-build-system)
514 (inputs `(("readline" ,readline)
515 ("cairo" ,cairo)
516 ("pango" ,pango)
6e64766a
DM		 517 ("gd" ,gd)
518 ("lua" ,lua)))
612a387f
RW		 519 (native-inputs
520 `(("pkg-config" ,pkg-config)
521 ("texlive" ,texlive-tiny)))
5f800540
KK		 522 (home-page "http://www.gnuplot.info")
523 (synopsis "Command-line driven graphing utility")
524 (description "Gnuplot is a portable command-line driven graphing
35b9e423 525utility. It was originally created to allow scientists and students to
73fed4f8 526visualize mathematical functions and data interactively, but has grown to
35b9e423 527support many non-interactive uses such as web scripting. It is also used as a
73fed4f8 528plotting engine by third-party applications like Octave.")
5f800540
KK		 529 ;; X11 Style with the additional restriction that derived works may only be
530 ;; distributed as patches to the original.
531 (license (license:fsf-free
532 "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
668c06ac 533
32f70e1f
TD		 534(define-public gctp
535 (package
536 (name "gctp")
537 (version "2.0.0")
538 (source
539 (origin
540 (method url-fetch)
541 (uri (string-append "https://github.com/OkoSanto/GCTP/archive/v"
542 version ".tar.gz"))
543 (file-name (string-append name "-" version ".tar.gz"))
544 (sha256
545 (base32
546 "0l9aqnqynh9laicn5dxf3rsb1n14xiks79wbyqccirzmjqd1c1x4"))))
547 (native-inputs
548 `(("fortran" ,gfortran)))
549 (build-system gnu-build-system)
550 (synopsis "General Cartographic Transformation Package (GCTP)")
551 (description
552 "The General Cartographic Transformation Package (GCTP) is a system of
553software routines designed to permit the transformation of coordinate pairs
554from one map projection to another. The GCTP is the standard computer
555software used by the National Mapping Division for map projection
556computations.")
557 (home-page "https://github.com/OkoSanto/GCTP")
0f7cd95b 558 (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
32f70e1f 559
becbbefc
TD		 560(define-public hdf4
561 (package
562 (name "hdf4")
7bbf2e39 563 (version "4.2.12")
becbbefc
TD		 564 (source
565 (origin
566 (method url-fetch)
567 (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
568 version "/src/hdf-" version ".tar.bz2"))
569 (sha256
7bbf2e39 570 (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id"))
15ca49b2
AE		 571 (patches (search-patches "hdf4-architectures.patch"
572 "hdf4-reproducibility.patch"
becbbefc
TD		 573 "hdf4-shared-fortran.patch"))))
574
575 (build-system gnu-build-system)
576 (native-inputs
577 `(("gfortran" ,gfortran)
578 ("bison" ,bison)
579 ("flex" ,flex)))
580 (inputs
581 `(("zlib" ,zlib)
582 ("libjpeg" ,libjpeg)))
583 (arguments
584 `(#:parallel-tests? #f
585 #:configure-flags '("--enable-shared")
586 #:phases
587 (modify-phases %standard-phases
588 (add-before 'configure 'patchbuild
589 (lambda _
590 (substitute*
591 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
592 (("/bin/rm") "rm")
593 (("/bin/mkdir") "mkdir"))
594 (substitute* (find-files "." "^Makefile\\.in$")
595 (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
596-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
597 (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
598-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
599-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
600 (home-page "https://www.hdfgroup.org/products/hdf4/")
601 (synopsis
602 "Library and multi-object file format for storing and managing data")
603 (description "HDF4 is a library and multi-object file format for storing
604and managing data between machines. HDF4 is an older hierarchical data format,
605incompatible with HDF5.")
606 (license
607 (license:non-copyleft
608 "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
609
610(define-public hdf4-alt
611 (package
612 (inherit hdf4)
613 (name "hdf4-alt")
614 (arguments
615 (substitute-keyword-arguments (package-arguments hdf4)
616 ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
617 (synopsis
618 "HDF4 without netCDF API, can be combined with the regular netCDF library")))
619
7ee3f1a2
JD		 620(define-public hdf5
621 (package
622 (name "hdf5")
2da63064 623 (version "1.8.19")
7ee3f1a2
JD		 624 (source
625 (origin
626 (method url-fetch)
2da63064
TD		 627 (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
628 "hdf5-" (version-major+minor version)
629 "/hdf5-" version "/src/hdf5-"
dcd9d163
LF		 630 version ".tar.bz2")
631 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
632 "current"
633 (apply string-append
634 (take (string-split version #\.) 2))
635 "/src/hdf5-" version ".tar.bz2")))
7ee3f1a2 636 (sha256
2da63064 637 (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r"))
b8d9c93b 638 (patches (list (search-patch "hdf5-config-date.patch")))))
7ee3f1a2 639 (build-system gnu-build-system)
12ed1216
AE		 640 (inputs
641 `(("zlib" ,zlib)))
7ee3f1a2 642 (arguments
62126576
LC		 643 `(;; Some of the users, notably Flann, need the C++ interface.
644 #:configure-flags '("--enable-cxx")
645
646 #:phases
f622e212
EB		 647 (modify-phases %standard-phases
648 (add-before 'configure 'patch-configure
649 (lambda _
650 (substitute* "configure"
b8d9c93b
EB		 651 (("/bin/mv") "mv"))
652 #t))
f622e212
EB		 653 (add-after 'install 'patch-references
654 (lambda* (#:key inputs outputs #:allow-other-keys)
655 (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
656 (zlib (assoc-ref inputs "zlib")))
657 (substitute* (find-files bin "h5p?cc")
658 (("-lz" lib)
659 (string-append "-L" zlib "/lib " lib)))
660 #t))))))
7ee3f1a2 661 (home-page "http://www.hdfgroup.org")
516e93f8 662 (synopsis "Management suite for extremely large and complex data")
7ee3f1a2
JD		 663 (description "HDF5 is a suite that makes possible the management of
664extremely large and complex data collections.")
d4bf49b1
EB		 665 (license (license:x11-style
666 "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
7ee3f1a2 667
d3c4f3bb
TD		 668(define-public hdf-eos2
669 (package
670 (name "hdf-eos2")
671 (version "19.1.0")
672 (source
673 (origin
674 (method url-fetch)
675 (uri "ftp://edhs1.gsfc.nasa.gov\
676/edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
677 (sha256
678 (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
679 (patches (search-patches "hdf-eos2-remove-gctp.patch"
680 "hdf-eos2-build-shared.patch"
681 "hdf-eos2-fortrantests.patch"))))
682 (build-system gnu-build-system)
683 (native-inputs
684 `(("gfortran" ,gfortran)))
685 (inputs
686 `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
687 ("zlib" ,zlib)
688 ("libjpeg" ,libjpeg)
689 ("gctp" ,gctp)))
690 (arguments
691 `( #:configure-flags '("--enable-install-include" "--enable-shared"
692 "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
693 #:parallel-tests? #f))
694 (home-page "http://hdfeos.org/software/library.php#HDF-EOS2")
695 (synopsis "HDF4-based data format for NASA's Earth Observing System")
696 (description "HDF-EOS2 is a software library built on HDF4 which supports
697the construction of data structures used in NASA's Earth Observing
698System (Grid, Point and Swath).")
699
700 ;; Source files carry a permissive license header.
701 (license (license:non-copyleft home-page))))
702
0f43f835
TD		 703(define-public hdf-eos5
704 (package
705 (name "hdf-eos5")
706 (version "1.15")
707 (source (origin
708 (method url-fetch)
709 (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
710/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
711 (sha256
712 (base32
713 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
714 (patches (search-patches "hdf-eos5-build-shared.patch"
715 "hdf-eos5-remove-gctp.patch"
716 "hdf-eos5-fix-szip.patch"
717 "hdf-eos5-fortrantests.patch"))))
718 (native-inputs
719 `(("gfortran" ,gfortran)))
720 (build-system gnu-build-system)
721 (inputs
722 `(("hdf5" ,hdf5)
723 ("zlib" ,zlib)
724 ("gctp" ,gctp)))
725 (arguments
726 `(#:configure-flags '("--enable-install-include" "--enable-shared"
727 "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
728 #:parallel-tests? #f))
729 (synopsis "HDF5-based data format for NASA's Earth Observing System")
730 (description
731 "HDF-EOS5 is a software library built on HDF5 to support the construction
732of data structures used in NASA's Earth Observing System (Grid, Point and
733Swath).")
734 (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
735
736 ;; Source files carry a permissive license header.
737 (license (license:non-copyleft home-page))))
738
c8378eea
EB		 739(define-public hdf5-parallel-openmpi
740 (package (inherit hdf5)
741 (name "hdf5-parallel-openmpi")
742 (inputs
743 `(("mpi" ,openmpi)
744 ,@(package-inputs hdf5)))
745 (arguments
746 (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
747 ,@(package-arguments hdf5))
748 ((#:phases phases)
749 `(modify-phases ,phases
750 (add-before 'check 'patch-tests
751 (lambda _
752 ;; OpenMPI's mpirun will exit with non-zero status if it
753 ;; detects an "abnormal termination", i.e. any process not
754 ;; calling MPI_Finalize(). Since the test is explicitely
755 ;; avoiding MPI_Finalize so as not to have at_exit and thus
756 ;; H5C_flush_cache from being called, mpirun will always
757 ;; complain, so turn this test off.
758 (substitute* "testpar/Makefile"
759 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
760 (string-append front back "\n")))
761 (substitute* "tools/h5diff/testph5diff.sh"
762 (("/bin/sh") (which "sh")))
763 #t))))))
764 (synopsis "Management suite for data with parallel IO support")))
765
00775104
EB		 766(define-public h5check
767 (package
768 (name "h5check")
769 (version "2.0.1")
770 (source
771 (origin
772 (method url-fetch)
773 (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
774 "h5check/src/h5check-" version ".tar.gz"))
775 (sha256
776 (base32
777 "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
778 (build-system gnu-build-system)
779 (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
780 (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
781 (synopsis "HDF5 format checker")
782 (description "@code{h5check} is a validation tool for verifying that an
783HDF5 file is encoded according to the HDF File Format Specification.")
784 (license (license:x11-style "file://COPYING"))))
785
a53d6719
JD		 786(define-public itpp
787 (package
788 (name "itpp")
789 (version "4.3.1")
790 (source (origin
791 (method url-fetch)
792 (uri (string-append "mirror://sourceforge/itpp/itpp/"
793 version "/itpp-"
794 version ".tar.gz"))
795 (sha256
796 (base32
797 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
798 (build-system cmake-build-system)
799 (arguments `(#:tests? #f)) ; Tests require googletest *sources*
800 (inputs `(("lapack" ,lapack)
801 ("fftw" ,fftw)))
3a4d5df2
RW		 802 ;; FIXME: Even though the fonts are available dvips complains:
803 ;; "Font cmmi10 not found; characters will be left blank."
804 (native-inputs
805 `(("texlive" ,texlive-tiny)
806 ("ghostscript" ,ghostscript)
807 ("doxygen" ,doxygen)))
a53d6719
JD		 808 (home-page "http://itpp.sourceforge.net")
809 (synopsis "C++ library of maths, signal processing and communication classes")
810 (description "IT++ is a C++ library of mathematical, signal processing and
811communication classes and functions. Its main use is in simulation of
812communication systems and for performing research in the area of
813communications. The kernel of the library consists of generic vector and
814matrix classes, and a set of accompanying routines. Such a kernel makes IT++
815similar to MATLAB, GNU Octave or SciPy.")
816 (license license:gpl3+)))
817
889187a4
EB		 818(define-public netcdf
819 (package
820 (name "netcdf")
a4b0bfb1 821 (version "4.4.1.1")
889187a4
EB		 822 (source
823 (origin
824 (method url-fetch)
825 (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
826 "netcdf-" version ".tar.gz"))
827 (sha256
828 (base32
a4b0bfb1
EB		 829 "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d"))
830 (patches (search-patches "netcdf-date-time.patch"
831 "netcdf-tst_h_par.patch"))))
889187a4
EB		 832 (build-system gnu-build-system)
833 (native-inputs
834 `(("m4" ,m4)
835 ("doxygen" ,doxygen)
836 ("graphviz" ,graphviz)))
837 (inputs
db825570
TD		 838 `(("hdf4" ,hdf4-alt)
839 ("hdf5" ,hdf5)
840 ("zlib" ,zlib)
841 ("libjpeg" ,libjpeg)))
889187a4 842 (arguments
db825570 843 `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
889187a4
EB		 844 #:parallel-tests? #f)) ;various race conditions
845 (home-page "http://www.unidata.ucar.edu/software/netcdf/")
846 (synopsis "Library for scientific data")
847 (description "NetCDF is an interface for scientific data access and a
848software library that provides an implementation of the interface. The netCDF
849library defines a machine-independent format for representing scientific data.
850Together, the interface, library, and format support the creation, access, and
851sharing of scientific data.")
852 (license (license:x11-style "file://COPYRIGHT"))))
853
854(define-public netcdf-parallel-openmpi
855 (package (inherit netcdf)
856 (name "netcdf-parallel-openmpi")
857 (inputs
858 `(("mpi" ,openmpi)
859 ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
860 (package-inputs netcdf))))
861 ;; TODO: Replace pkg-config references in nc-config with absolute references
862 (arguments
863 (substitute-keyword-arguments (package-arguments netcdf)
864 ((#:configure-flags flags)
865 `(cons* "CC=mpicc" "CXX=mpicxx"
866 "--enable-parallel-tests"
867 ;; Shared libraries not supported with parallel IO.
868 "--disable-shared" "--with-pic"
869 ,flags))))))
870
300200b6
TD		 871(define-public netcdf-fortran
872 (package
873 (name "netcdf-fortran")
874 (version "4.4.4")
875 (source (origin
876 (method url-fetch)
877 (uri (string-append
878 "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
879 version ".tar.gz"))
880 (sha256
881 (base32
882 "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj"))))
883 (build-system gnu-build-system)
884 (arguments
885 `(#:parallel-tests? #f))
886 (inputs
887 `(("netcdf" ,netcdf)))
888 (native-inputs
889 `(("gfortran" ,gfortran)))
890 (synopsis "Fortran interface for the netCDF library")
891 (description (package-description netcdf))
892 (home-page (package-home-page netcdf))
893 (license (package-license netcdf))))
894
1b39a196
RJ		 895(define-public nlopt
896 (package
897 (name "nlopt")
898 (version "2.4.2")
899 (source (origin
900 (method url-fetch)
901 (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
902 version ".tar.gz"))
903 (sha256
904 (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
905 (build-system gnu-build-system)
906 (arguments
907 `(;; Shared libraries are not built by default. They are required to
908 ;; build the Guile, Octave, and Python bindings.
909 #:configure-flags '("--enable-shared")
910
911 #:phases
912 (modify-phases %standard-phases
913 (add-before 'configure 'set-libnlopt-file-name
914 (lambda* (#:key outputs #:allow-other-keys)
915 ;; Make sure the Scheme module refers to the library by its
916 ;; absolute file name (we cannot do that from a snippet
917 ;; because the expansion of @libdir@ contains
918 ;; ${exec_prefix}.)
919 (let ((out (assoc-ref outputs "out")))
920 (substitute* "swig/nlopt.scm.in"
921 (("libnlopt")
922 (string-append out "/lib/libnlopt")))
923 #t))))))
924 (inputs `(("guile" ,guile-2.0)))
925 (native-inputs `(("pkg-config" ,pkg-config)))
926 (home-page "http://ab-initio.mit.edu/wiki/")
927 (synopsis "Library for nonlinear optimization")
928 (description "NLopt is a library for nonlinear optimization, providing a
929common interface for a number of different free optimization routines available
930online as well as original implementations of various other algorithms.")
931 (license license:lgpl2.1+)))
932
005c787d
LC		 933(define-public ipopt
934 (package
935 (name "ipopt")
936 (version "3.12.5")
937 (source (origin
938 (method url-fetch)
939 (uri (string-append
940 "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
941 version".tgz"))
942 (sha256
943 (base32
944 "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
945 (modules '((guix build utils)))
946 (snippet
947 ;; Make sure we don't use the bundled software.
948 '(delete-file-recursively "ThirdParty"))))
949 (build-system gnu-build-system)
ad1c4537
LC		 950 (arguments
951 '(#:phases (modify-phases %standard-phases
952 (add-after 'install 'add--L-flags-in-ipopt.pc
953 (lambda* (#:key inputs outputs #:allow-other-keys)
954 ;; The '.pc' file lists '-llapack -lblas' in "Libs";
955 ;; move it to "Libs.private" where it belongs, and add a
956 ;; '-L' flag for LAPACK.
957 (let ((out (assoc-ref outputs "out"))
958 (lapack (assoc-ref inputs "lapack")))
959 (substitute* (string-append out "/lib/pkgconfig/"
960 "ipopt.pc")
961 (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
962 (string-append "Libs: " before " " after "\n"
963 "Libs.private: " before
964 "-L" lapack "/lib -llapack -lblas "
965 after "\n")))
966 #t))))))
005c787d
LC		 967 (native-inputs
968 `(("gfortran" ,gfortran)))
969 (inputs
970 ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
ad1c4537 971 `(("lapack" ,lapack))) ;for both libblas and liblapack
005c787d
LC		 972 (home-page "http://www.coin-or.org")
973 (synopsis "Large-scale nonlinear optimizer")
974 (description
975 "The Interior Point Optimizer (IPOPT) is a software package for
976large-scale nonlinear optimization. It provides C++, C, and Fortran
977interfaces.")
978 (license license:epl1.0)))
979
f9940ef1
LC		 980(define-public ceres
981 (package
982 (name "ceres-solver")
983 (version "1.11.0")
984 (home-page "http://ceres-solver.org/")
985 (source (origin
986 (method url-fetch)
987 (uri (string-append home-page "ceres-solver-"
988 version ".tar.gz"))
989 (sha256
990 (base32
991 "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
992 (build-system cmake-build-system)
993 (arguments
994 ;; TODO: Build HTML user documentation and install separately.
bc3a2e35 995 '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
f9940ef1
LC		 996 "-DBUILD_SHARED_LIBS=ON")
997
998 #:phases (modify-phases %standard-phases
999 (add-before 'configure 'set-library-directory
1000 (lambda _
1001 ;; Install libraries to lib/, not lib64/.
1002 (substitute* "internal/ceres/CMakeLists.txt"
1003 (("set\\(LIB_SUFFIX \"64\"\\)")
1004 "set(LIB_SUFFIX \"\")"))
1005 #t)))))
1006 (native-inputs
1007 `(("pkg-config" ,pkg-config)))
468e0b18
LC		 1008 (propagated-inputs
1009 `(("glog" ,glog))) ;for #include <glog/glog.h>
f9940ef1
LC		 1010 (inputs
1011 `(("eigen" ,eigen)
1012 ("blas" ,openblas)
1013 ("lapack" ,lapack)
1014 ("suitesparse" ,suitesparse)
1015 ("gflags" ,gflags)))
1016 (synopsis "C++ library for solving large optimization problems")
1017 (description
1018 "Ceres Solver is a C++ library for modeling and solving large,
1019complicated optimization problems. It is a feature rich, mature and
1020performant library which has been used in production since 2010. Ceres Solver
1021can solve two kinds of problems:
1022@enumerate
1023@item non-linear least squares problems with bounds constraints;
1024@item general unconstrained optimization problems.
1025@end enumerate\n")
1026 (license license:bsd-3)))
1027
668c06ac
JD		 1028;; For a fully featured Octave, users are strongly recommended also to install
1029;; the following packages: texinfo, less, ghostscript, gnuplot.
1030(define-public octave
1031 (package
1032 (name "octave")
e9d60eba 1033 (version "4.2.1")
668c06ac
JD		 1034 (source
1035 (origin
1036 (method url-fetch)
1037 (uri (string-append "mirror://gnu/octave/octave-"
f5a077b1 1038 version ".tar.lz"))
668c06ac
JD		 1039 (sha256
1040 (base32
e9d60eba 1041 "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92"))))
668c06ac
JD		 1042 (build-system gnu-build-system)
1043 (inputs
1044 `(("lapack" ,lapack)
1045 ("readline" ,readline)
181170c6 1046 ("gl2ps" ,gl2ps)
668c06ac 1047 ("glpk" ,glpk)
1ec78e9d
EB		 1048 ("fftw" ,fftw)
1049 ("fftwf" ,fftwf)
1050 ("arpack" ,arpack-ng)
668c06ac
JD		 1051 ("pcre" ,pcre)
1052 ("fltk" ,fltk)
1053 ("fontconfig" ,fontconfig)
1054 ("freetype" ,freetype)
40029cbe 1055 ("hdf5" ,hdf5)
668c06ac
JD		 1056 ("libxft" ,libxft)
1057 ("mesa" ,mesa)
1ec78e9d 1058 ("glu" ,glu)
9f913401
AI		 1059 ("zlib" ,zlib)
1060 ("curl" ,curl)
1061 ("graphicsmagick" ,graphicsmagick)))
668c06ac 1062 (native-inputs
f5a077b1
EF		 1063 `(("lzip" ,lzip)
1064 ("gfortran" ,gfortran)
668c06ac
JD		 1065 ("pkg-config" ,pkg-config)
1066 ("perl" ,perl)
1ec78e9d
EB		 1067 ;; The following inputs are not actually used in the build process.
1068 ;; However, the ./configure gratuitously tests for their existence and
1069 ;; assumes that programs not present at build time are also not, and
1070 ;; can never be, available at run time! If these inputs are therefore
1071 ;; not present, support for them will be built out. However, Octave
1072 ;; will still run without them, albeit without the features they
668c06ac
JD		 1073 ;; provide.
1074 ("less" ,less)
1075 ("texinfo" ,texinfo)
1076 ("ghostscript" ,ghostscript)
1077 ("gnuplot" ,gnuplot)))
1078 (arguments
b7b27a8f
KY		 1079 `(#:configure-flags
1080 (list (string-append "--with-shell="
1081 (assoc-ref %build-inputs "bash")
1082 "/bin/sh"))))
f5a077b1 1083 (home-page "https://www.gnu.org/software/octave/")
668c06ac 1084 (synopsis "High-level language for numerical computation")
1ec78e9d
EB		 1085 (description "GNU Octave is a high-level interpreted language that is
1086specialized for numerical computations. It can be used for both linear and
1087non-linear applications and it provides great support for visualizing results.
1088Work may be performed both at the interactive command-line as well as via
1089script files.")
668c06ac 1090 (license license:gpl3+)))
3de01d3f 1091
5d4bd4cc
PG		 1092(define-public opencascade-oce
1093 (package
1094 (name "opencascade-oce")
1095 (version "0.17.2")
1096 (source
1097 (origin
1098 (method url-fetch)
1099 (uri (string-append
1100 "https://github.com/tpaviot/oce/archive/OCE-"
1101 version
1102 ".tar.gz"))
1103 (sha256
1104 (base32
1105 "0vpmnb0k5y2f7lpmwx9pg9yfq24zjvnsak5alzacncfm1hv9b6cd"))))
1106 (build-system cmake-build-system)
1107 (arguments
1108 '(#:configure-flags
1109 (list "-DOCE_TESTING:BOOL=ON"
1110 "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
1111 "-DOCE_DRAW:BOOL=ON"
1112 (string-append "-DOCE_INSTALL_PREFIX:PATH="
1113 (assoc-ref %outputs "out"))
1114 "-UCMAKE_INSTALL_RPATH")))
1115 (inputs
1116 `(("freetype" ,freetype)
1117 ("glu" ,glu)
1118 ("libxmu" ,libxmu)
1119 ("mesa" ,mesa)
1120 ("tcl" ,tcl)
1121 ("tk" ,tk)))
1122 (native-inputs
1123 `(("python" ,python-wrapper)))
1124 (home-page "https://github.com/tpaviot/oce")
1125 (synopsis "Libraries for 3D modeling and numerical simulation")
1126 (description
1127 "Open CASCADE is a set of libraries for the development of applications
1128dealing with 3D CAD data or requiring industrial 3D capabilities. It includes
1129C++ class libraries providing services for 3D surface and solid modeling, CAD
1130data exchange, and visualization. It is used for development of specialized
1131software dealing with 3D models in design (CAD), manufacturing (CAM),
1132numerical simulation (CAE), measurement equipment (CMM), and quality
1133control (CAQ) domains.
1134
1135This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
1136patches, improvements, and experiments contributed by users over the official
1137Open CASCADE library.")
1138 (license (list license:lgpl2.1; OCE libraries, with an exception for the
1139 ; use of header files; see
1140 ; OCCT_LGPL_EXCEPTION.txt
1141 license:public-domain; files
1142 ; src/Standard/Standard_StdAllocator.hxx and
1143 ; src/NCollection/NCollection_StdAllocator.hxx
1144 license:expat; file src/OpenGl/OpenGl_glext.h
1145 license:bsd-3)))); test framework gtest
1146
3de01d3f
EB		 1147(define-public gmsh
1148 (package
1149 (name "gmsh")
8a4d14fa 1150 (version "2.16.0")
3de01d3f
EB		 1151 (source
1152 (origin
1153 (method url-fetch)
1c79e086 1154 (uri (string-append "http://gmsh.info/src/gmsh-"
3de01d3f
EB		 1155 version "-source.tgz"))
1156 (sha256
8a4d14fa 1157 (base32 "1slf0bfkwrcgn6296wb4qhbk4ahz6i4wfb10hnim08x05vrylag8"))
3de01d3f
EB		 1158 (modules '((guix build utils)))
1159 (snippet
1160 ;; Remove non-free METIS code
1161 '(delete-file-recursively "contrib/Metis"))))
1162 (build-system cmake-build-system)
3de01d3f
EB		 1163 (propagated-inputs
1164 `(("fltk" ,fltk)
19afbea1 1165 ("gfortran" ,gfortran)
3de01d3f 1166 ("gmp" ,gmp)
40029cbe 1167 ("hdf5" ,hdf5)
3de01d3f
EB		 1168 ("lapack" ,lapack)
1169 ("mesa" ,mesa)
85f41902 1170 ("glu" ,glu)
45548139 1171 ("opencascade-oce" ,opencascade-oce)
3de01d3f
EB		 1172 ("libx11" ,libx11)
1173 ("libxext" ,libxext)))
66395a61
EF		 1174 (inputs
1175 `(("fontconfig" ,fontconfig)
1176 ("libxft" ,libxft)))
3de01d3f
EB		 1177 (arguments
1178 `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
1179 "-DENABLE_BUILD_SHARED:BOOL=ON"
45548139 1180 "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
3de01d3f
EB		 1181 (home-page "http://www.geuz.org/gmsh/")
1182 (synopsis "3D finite element grid generator")
edf684ef
EB		 1183 (description "Gmsh is a 3D finite element grid generator with a built-in
1184CAD engine and post-processor. Its design goal is to provide a fast, light
1185and user-friendly meshing tool with parametric input and advanced
1186visualization capabilities. Gmsh is built around four modules: geometry,
1187mesh, solver and post-processing. The specification of any input to these
1188modules is done either interactively using the graphical user interface or in
1189ASCII text files using Gmsh's own scripting language.")
3de01d3f 1190 (license license:gpl2+)))
b9100e2f 1191
6d5f63b6
JD		 1192(define-public maxflow
1193 (package
1194 (name "maxflow")
1195 (version "3.04")
1196 (source (origin
1197 (method git-fetch)
1198 (uri (git-reference
1199 (url "https://github.com/gerddie/maxflow.git")
1200 (commit "42401fa54823d16b9da47716f04e5d9ef1605875")))
1201 (file-name (string-append name "-" version "-checkout"))
1202 (sha256
1203 (base32
1204 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
1205 (build-system cmake-build-system)
1206 (home-page "http://pub.ist.ac.at/~vnk/software.html")
1207 (synopsis "Library implementing Maxflow algorithm")
1208 (description "An implementation of the maxflow algorithm described in
1209@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
1210Energy Minimization in Computer Vision.\n
1211Yuri Boykov and Vladimir Kolmogorov.\n
1212In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
1213September 2004}")
1214 (license license:gpl3+)))
1215
b9100e2f
EB		 1216(define-public petsc
1217 (package
1218 (name "petsc")
fafd623e 1219 (version "3.7.2")
b9100e2f
EB		 1220 (source
1221 (origin
1222 (method url-fetch)
1223 ;; The *-lite-* tarball does not contain the *large* documentation
1224 (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
1225 "petsc-lite-" version ".tar.gz"))
1226 (sha256
fafd623e 1227 (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
b9100e2f
EB		 1228 (build-system gnu-build-system)
1229 (native-inputs
1230 `(("python" ,python-2)
1231 ("perl" ,perl)))
1232 (inputs
19afbea1 1233 `(("gfortran" ,gfortran)
b9100e2f 1234 ("lapack" ,lapack)
f258212d 1235 ("superlu" ,superlu)
b9100e2f
EB		 1236 ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
1237 ;; leaving out opengl, as configuration seems to only be for mac
1238 ))
1239 (arguments
1240 `(#:test-target "test"
9a899cce 1241 #:parallel-build? #f ;build is parallel by default
b9100e2f
EB		 1242 #:configure-flags
1243 `("--with-mpi=0"
f258212d
EB		 1244 "--with-openmp=1"
1245 "--with-superlu=1"
1246 ,(string-append "--with-superlu-include="
1247 (assoc-ref %build-inputs "superlu") "/include")
1248 ,(string-append "--with-superlu-lib="
1249 (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
b9100e2f 1250 #:phases
64dcc289
EB		 1251 (modify-phases %standard-phases
1252 (replace 'configure
1253 ;; PETSc's configure script is actually a python script, so we can't
1254 ;; run it with bash.
1255 (lambda* (#:key outputs (configure-flags '())
1256 #:allow-other-keys)
1257 (let* ((prefix (assoc-ref outputs "out"))
1258 (flags `(,(string-append "--prefix=" prefix)
1259 ,@configure-flags)))
1260 (format #t "build directory: ~s~%" (getcwd))
1261 (format #t "configure flags: ~s~%" flags)
1262 (zero? (apply system* "./configure" flags)))))
1263 (add-after 'configure 'clean-local-references
64dcc289
EB		 1264 (lambda* (#:key inputs outputs #:allow-other-keys)
1265 (let ((out (assoc-ref outputs "out")))
1266 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
b730b437
EB		 1267 ;; Prevent build directory from leaking into compiled code
1268 (((getcwd)) out)
1269 ;; Scrub timestamp for reproducibility
fafd623e
EB		 1270 ((".*Libraries compiled on.*") ""))
1271 #t)))
64dcc289 1272 (add-after 'install 'clean-install
10b11968
EB		 1273 ;; Try to keep installed files from leaking build directory names.
1274 (lambda* (#:key inputs outputs #:allow-other-keys)
64dcc289 1275 (let ((out (assoc-ref outputs "out")))
10b11968 1276 (substitute* (map (lambda (file)
9a899cce 1277 (string-append out "/lib/petsc/conf/" file))
fafd623e 1278 '("petscvariables"))
10b11968
EB		 1279 (((getcwd)) out))
1280 ;; Make compiler references point to the store
9a899cce 1281 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
dfdf5716
EB		 1282 (("= (gcc|g\\+\\+|gfortran)" _ compiler)
1283 (string-append "= " (which compiler))))
10b11968
EB		 1284 ;; PETSc installs some build logs, which aren't necessary.
1285 (for-each (lambda (file)
9a899cce 1286 (let ((f (string-append out "/lib/petsc/conf/" file)))
10b11968
EB		 1287 (when (file-exists? f)
1288 (delete-file f))))
9a899cce
EB		 1289 '("configure.log" "make.log" "gmake.log"
1290 "test.log" "error.log" "RDict.db"
fafd623e 1291 "PETScBuildInternal.cmake"
10b11968 1292 ;; Once installed, should uninstall with Guix
fafd623e
EB		 1293 "uninstall.py"))
1294 #t))))))
b9100e2f 1295 (home-page "http://www.mcs.anl.gov/petsc")
16ecf3ff 1296 (synopsis "Library to solve PDEs")
b9100e2f
EB		 1297 (description "PETSc, pronounced PET-see (the S is silent), is a suite of
1298data structures and routines for the scalable (parallel) solution of
1299scientific applications modeled by partial differential equations.")
166191b3 1300 (license (license:non-copyleft
b9100e2f
EB		 1301 "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
1302
1303(define-public petsc-complex
1304 (package (inherit petsc)
1305 (name "petsc-complex")
1306 (arguments
1307 (substitute-keyword-arguments (package-arguments petsc)
1308 ((#:configure-flags cf)
1309 `(cons "--with-scalar-type=complex" ,cf))))
16ecf3ff 1310 (synopsis "Library to solve PDEs (with complex scalars)")))
183e44ae 1311
d8c7eeb9
EB		 1312(define-public petsc-openmpi
1313 (package (inherit petsc)
1314 (name "petsc-openmpi")
1315 (inputs
1316 `(("openmpi" ,openmpi)
1317 ,@(package-inputs petsc)))
1318 (arguments
1319 (substitute-keyword-arguments (package-arguments petsc)
1320 ((#:configure-flags cf)
1321 ``("--with-mpiexec=mpirun"
1322 ,(string-append "--with-mpi-dir="
1323 (assoc-ref %build-inputs "openmpi"))
1324 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1325 (synopsis "Library to solve PDEs (with MPI support)")))
d8c7eeb9
EB		 1326
1327(define-public petsc-complex-openmpi
1328 (package (inherit petsc-complex)
1329 (name "petsc-complex-openmpi")
1330 (inputs
1331 `(("openmpi" ,openmpi)
1332 ,@(package-inputs petsc-complex)))
1333 (arguments
1334 (substitute-keyword-arguments (package-arguments petsc-complex)
1335 ((#:configure-flags cf)
1336 ``("--with-mpiexec=mpirun"
1337 ,(string-append "--with-mpi-dir="
1338 (assoc-ref %build-inputs "openmpi"))
1339 ,@(delete "--with-mpi=0" ,cf)))))
16ecf3ff 1340 (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
d8c7eeb9 1341
a7f01414
EB		 1342(define-public slepc
1343 (package
1344 (name "slepc")
8787c555 1345 (version "3.7.1")
a7f01414
EB		 1346 (source
1347 (origin
1348 (method url-fetch)
1349 (uri (string-append "http://slepc.upv.es/download/download.php?"
1350 "filename=slepc-" version ".tar.gz"))
d588422e 1351 (file-name (string-append name "-" version ".tar.gz"))
a7f01414
EB		 1352 (sha256
1353 (base32
8787c555 1354 "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
a7f01414
EB		 1355 (build-system gnu-build-system)
1356 (native-inputs
1357 `(("python" ,python-2)))
1358 (inputs
1359 `(("arpack" ,arpack-ng)
1360 ("gfortran" ,gfortran)))
1361 (propagated-inputs
1362 `(("petsc" ,petsc)))
1363 (arguments
1364 `(#:parallel-build? #f ;build is parallel by default
1365 #:configure-flags
1366 `(,(string-append "--with-arpack-dir="
9cf52454 1367 (assoc-ref %build-inputs "arpack") "/lib"))
a7f01414
EB		 1368 #:phases
1369 (modify-phases %standard-phases
8787c555 1370 (replace 'configure
a7f01414
EB		 1371 ;; configure is a python script, so we can't run it with bash.
1372 (lambda* (#:key inputs outputs (configure-flags '())
1373 #:allow-other-keys)
1374 (let* ((prefix (assoc-ref outputs "out"))
1375 (flags `(,(string-append "--prefix=" prefix)
1376 ,@configure-flags)))
1377 (format #t "build directory: ~s~%" (getcwd))
1378 (format #t "configure flags: ~s~%" flags)
1379 (setenv "SLEPC_DIR" (getcwd))
9cf52454 1380 (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
a7f01414 1381 (zero? (apply system* "./configure" flags)))))
8787c555 1382 (add-after 'install 'delete-doc
a7f01414
EB		 1383 ;; TODO: SLEPc installs HTML documentation alongside headers in
1384 ;; $out/include. We'd like to move them to share/doc, but delete
1385 ;; them for now, as they are incomplete and installing the complete
1386 ;; documentation is difficult.
1387 (lambda* (#:key outputs #:allow-other-keys)
1388 (let* ((out (assoc-ref outputs "out")))
1389 (for-each delete-file (find-files out "\\.html$")))))
8787c555 1390 (add-after 'install 'clean-install
a7f01414
EB		 1391 ;; Clean up unnecessary build logs from installation.
1392 (lambda* (#:key outputs #:allow-other-keys)
1393 (let ((out (assoc-ref outputs "out")))
1394 (for-each (lambda (file)
1395 (let ((f (string-append out "/lib/slepc/conf/" file)))
1396 (when (file-exists? f)
1397 (delete-file f))))
1398 '("configure.log" "make.log" "gmake.log"
1399 "test.log" "error.log" "RDict.db"
1400 "uninstall.py"))))))))
1401 (home-page "http://slepc.upv.es")
1402 (synopsis "Scalable library for eigenproblems")
1403 (description "SLEPc is a software library for the solution of large sparse
1404eigenproblems on parallel computers. It can be used for the solution of
1405linear eigenvalue problems formulated in either standard or generalized form,
1406as well as other related problems such as the singular value decomposition.
1407The emphasis of the software is on methods and techniques appropriate for
1408problems in which the associated matrices are sparse, for example, those
1409arising after the discretization of partial differential equations.")
1410 (license license:lgpl3)))
1411
1412(define-public slepc-complex
1413 (package (inherit slepc)
1414 (name "slepc-complex")
1415 (propagated-inputs
1416 `(("petsc" ,petsc-complex)
1417 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1418 (synopsis "Scalable library for eigenproblems (with complex scalars)")))
1419
1420(define-public slepc-openmpi
1421 (package (inherit slepc)
1422 (name "slepc-openmpi")
1423 (inputs
1424 `(("mpi" ,openmpi)
1425 ("arpack" ,arpack-ng-openmpi)
1426 ,@(alist-delete "arpack" (package-inputs slepc))))
1427 (propagated-inputs
1428 `(("petsc" ,petsc-openmpi)
1429 ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
1430 (synopsis "Scalable library for eigenproblems (with MPI support)")))
1431
1432(define-public slepc-complex-openmpi
1433 (package (inherit slepc-openmpi)
1434 (name "slepc-complex-openmpi")
1435 (propagated-inputs
1436 `(("petsc" ,petsc-complex-openmpi)
1437 ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
1438 (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
1439
cec86422
EB		 1440(define-public mumps
1441 (package
1442 (name "mumps")
fba78d18 1443 (version "5.0.2")
cec86422
EB		 1444 (source
1445 (origin
1446 (method url-fetch)
1447 (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
1448 version ".tar.gz"))
1449 (sha256
1450 (base32
fba78d18 1451 "0igyc1pfzxdhpbad3v3lb86ixkdbqa1a8gbs15b04r2294h2nabp"))
fc1adab1 1452 (patches (search-patches "mumps-build-parallelism.patch"))))
cec86422
EB		 1453 (build-system gnu-build-system)
1454 (inputs
1455 `(("fortran" ,gfortran)
1456 ;; These are required for linking against mumps, but we let the user
1457 ;; declare the dependency.
1458 ("blas" ,openblas)
1459 ("metis" ,metis)
1460 ("scotch" ,scotch)))
1461 (arguments
1462 `(#:modules ((ice-9 match)
1463 (ice-9 popen)
1464 (srfi srfi-1)
1465 ,@%gnu-build-system-modules)
1466 #:phases
1467 (modify-phases %standard-phases
fba78d18 1468 (replace 'configure
cec86422
EB		 1469 (lambda* (#:key inputs #:allow-other-keys)
1470 (call-with-output-file "Makefile.inc"
1471 (lambda (port)
1472 (format port "
1473PLAT =
1474LIBEXT = .a
1475OUTC = -o
1476OUTF = -o
1477RM = rm -f~:[
1478CC = gcc
1479FC = gfortran
1480FL = gfortran
1481INCSEQ = -I$(topdir)/libseq
1482LIBSEQ = -L$(topdir)/libseq -lmpiseq
1483LIBSEQNEEDED = libseqneeded~;
1484CC = mpicc
1485FC = mpifort
1486FL = mpifort~]
1487AR = ar vr # rules require trailing space, ugh...
1488RANLIB = ranlib
1489LIBBLAS = -L~a -lopenblas~@[
1490SCALAP = -L~a -lscalapack~]
1491LIBOTHERS = -pthread
1492CDEFS = -DAdd_
1493PIC = -fPIC
1494OPTF = -O2 -DALLOW_NON_INIT $(PIC)
1495OPTL = -O2 $(PIC)
1496OPTC = -O2 $(PIC)
1497INCS = $(INCSEQ)
1498LIBS = $(SCALAP) $(LIBSEQ)
1499LPORDDIR = $(topdir)/PORD/lib
1500IPORD = -I$(topdir)/PORD/include
1501LPORD = -L$(LPORDDIR) -lpord
1502ORDERINGSF = -Dpord~@[
1503METISDIR = ~a
1504IMETIS = -I$(METISDIR)/include
1505LMETIS = -L$(METISDIR)/lib -lmetis
1506ORDERINGSF += -Dmetis~]~@[~:{
1507SCOTCHDIR = ~a
1508ISCOTCH = -I$(SCOTCHDIR)/include
1509LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
1510ORDERINGSF += ~a~}~]
1511ORDERINGSC = $(ORDERINGSF)
1512LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
1513IORDERINGSF = $(ISCOTCH)
1514IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
1515 (assoc-ref inputs "mpi")
1516 (assoc-ref inputs "blas")
1517 (assoc-ref inputs "scalapack")
1518 (assoc-ref inputs "metis")
1519 (match (list (assoc-ref inputs "pt-scotch")
1520 (assoc-ref inputs "scotch"))
1521 ((#f #f)
1522 #f)
1523 ((#f scotch)
1524 `((,scotch "" "-Dscotch")))
1525 ((ptscotch _)
1526 `((,ptscotch
1527 "-lptesmumps -lptscotch -lptscotcherr "
1528 "-Dptscotch")))))))))
fba78d18 1529 (replace 'build
cec86422
EB		 1530 ;; By default only the d-precision library is built. Make with "all"
1531 ;; target so that all precision libraries and examples are built.
1532 (lambda _
1533 (zero? (system* "make" "all"
1534 (format #f "-j~a" (parallel-job-count))))))
fba78d18 1535 (replace 'check
cec86422
EB		 1536 ;; Run the simple test drivers, which read test input from stdin:
1537 ;; from the "real" input for the single- and double-precision
1538 ;; testers, and from the "cmplx" input for complex-precision
1539 ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
1540 ;; package to prefix execution with "mpirun".
1541 (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
1542 (with-directory-excursion "examples"
1543 (every
1544 (lambda (prec type)
1545 (let ((tester (apply open-pipe*
1546 `(,OPEN_WRITE
1547 ,@exec-prefix
1548 ,(string-append "./" prec
1549 "simpletest"))))
1550 (input (open-input-file
1551 (string-append "input_simpletest_" type))))
1552 (begin
1553 (dump-port input tester)
1554 (close-port input)
1555 (zero? (close-pipe tester)))))
1556 '("s" "d" "c" "z")
1557 '("real" "real" "cmplx" "cmplx")))))
fba78d18
EB		 1558 (replace 'install
1559 (lambda* (#:key outputs #:allow-other-keys)
1560 (let* ((out (assoc-ref outputs "out"))
1561 (libdir (string-append out "/lib")))
1562 (copy-recursively "lib" libdir)
1563 (copy-recursively "include" (string-append out "/include"))
1564 (when (file-exists? "libseq/libmpiseq.a")
1565 (install-file "libseq/libmpiseq.a" libdir))
1566 #t))))))
cec86422
EB		 1567 (home-page "http://mumps.enseeiht.fr")
1568 (synopsis "Multifrontal sparse direct solver")
1569 (description
1570 "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
1571sparse system of linear equations A x = b using Guassian elimination.")
1572 (license license:cecill-c)))
1573
1574(define-public mumps-metis
1575 (package (inherit mumps)
1576 (name "mumps-metis")
1577 (inputs
1578 (alist-delete "scotch" (package-inputs mumps)))))
1579
1580(define-public mumps-openmpi
1581 (package (inherit mumps)
1582 (name "mumps-openmpi")
1583 (inputs
1584 `(("mpi" ,openmpi)
1585 ("scalapack" ,scalapack)
1586 ("pt-scotch" ,pt-scotch)
1587 ,@(alist-delete "scotch" (package-inputs mumps))))
1588 (arguments
1589 (substitute-keyword-arguments (package-arguments mumps)
1590 ((#:phases phases)
1591 `(modify-phases ,phases
1592 (replace
1593 'check
1594 (lambda _
1595 ((assoc-ref ,phases 'check)
1596 #:exec-prefix '("mpirun" "-n" "2"))))))))
1597 (synopsis "Multifrontal sparse direct solver (with MPI)")))
1598
1599(define-public mumps-metis-openmpi
1600 (package (inherit mumps-openmpi)
1601 (name "mumps-metis-openmpi")
1602 (inputs
1603 (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
1604
2d047896
RW		 1605(define-public r-quadprog
1606 (package
1607 (name "r-quadprog")
1608 (version "1.5-5")
1609 (source
1610 (origin
1611 (method url-fetch)
1612 (uri (cran-uri "quadprog" version))
1613 (sha256
1614 (base32
1615 "0jg3r6abmhp8r9vkbhpx9ldjfw6vyl1m4c5vwlyjhk1mi03656fr"))))
1616 (build-system r-build-system)
1617 (native-inputs
1618 `(("gfortran" ,gfortran)))
1619 (home-page "http://cran.r-project.org/web/packages/quadprog")
1620 (synopsis "Functions to solve quadratic programming problems")
1621 (description
1622 "This package contains routines and documentation for solving quadratic
1623programming problems.")
1624 (license license:gpl3+)))
1625
ec8c7e47
RJ		 1626(define-public r-pracma
1627 (package
1628 (name "r-pracma")
2fe41e0f 1629 (version "2.0.4")
ec8c7e47
RJ		 1630 (source (origin
1631 (method url-fetch)
1632 (uri (cran-uri "pracma" version))
1633 (sha256
2fe41e0f 1634 (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc"))))
ec8c7e47 1635 (build-system r-build-system)
ccd9b151
RW		 1636 (propagated-inputs
1637 `(("r-quadprog" ,r-quadprog)))
ec8c7e47
RJ		 1638 (home-page "http://cran.r-project.org/web/packages/pracma")
1639 (synopsis "Practical numerical math functions")
1640 (description "This package provides functions for numerical analysis and
1641linear algebra, numerical optimization, differential equations, plus some
1642special functions. It uses Matlab function names where appropriate to simplify
1643porting.")
1644 (license license:gpl3+)))
1645
183e44ae
EB		 1646(define-public superlu
1647 (package
1648 (name "superlu")
995a09e0 1649 (version "5.2.1")
183e44ae
EB		 1650 (source
1651 (origin
1652 (method url-fetch)
1653 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1654 "superlu_" version ".tar.gz"))
1655 (sha256
995a09e0
EB		 1656 (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
1657 (modules '((guix build utils)))
1658 (snippet
1659 ;; Replace the non-free implementation of MC64 with a stub adapted
1660 ;; from Debian
1661 '(begin
1662 (use-modules (ice-9 regex)
1663 (ice-9 rdelim))
1664 (call-with-output-file "SRC/mc64ad.c"
1665 (lambda (port)
1666 (display "
1667#include <stdio.h>
1668#include <stdlib.h>
1669void mc64id_(int *a) {
1670 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1671 abort ();
1672}
1673void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1674 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1675 fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
1676 abort ();
1677}\n" port)))
1678 ;; Remove the corresponding license verbiage. MC64 license follows
1679 ;; a "------" line separator.
1680 (with-atomic-file-replacement "License.txt"
1681 (let ((rx (make-regexp "-{8}")))
1682 (lambda (in out)
1683 (let loop ()
1684 (let ((line (read-line in 'concat)))
1685 (unless (regexp-exec rx line)
1686 (display line out)
1687 (loop)))))))))))
1688 (build-system cmake-build-system)
183e44ae
EB		 1689 (native-inputs
1690 `(("tcsh" ,tcsh)))
1691 (inputs
995a09e0 1692 `(("blas" ,openblas)
19afbea1 1693 ("gfortran" ,gfortran)))
183e44ae 1694 (arguments
995a09e0
EB		 1695 `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
1696 "-DTPL_BLAS_LIBRARIES=openblas"
1697 "-DBUILD_SHARED_LIBS:BOOL=YES"
1698 "-DCMAKE_INSTALL_LIBDIR=lib")))
183e44ae
EB		 1699 (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
1700 (synopsis "Supernodal direct solver for sparse linear systems")
1701 (description
1702 "SuperLU is a general purpose library for the direct solution of large,
1703sparse, nonsymmetric systems of linear equations on high performance machines.
1704The library is written in C and is callable from either C or Fortran. The
1705library routines perform an LU decomposition with partial pivoting and
1706triangular system solves through forward and back substitution. The library
1707also provides threshold-based ILU factorization preconditioners.")
995a09e0
EB		 1708 (license (list license:bsd-3
1709 license:gpl2+ ;EXAMPLE/*fgmr.c
1710 (license:fsf-free "file://SRC/colamd.h")))))
f8ed036a 1711
a54aefea
EB		 1712(define-public superlu-dist
1713 (package
1714 (name "superlu-dist")
1715 (version "3.3")
1716 (source
1717 (origin
1718 (method url-fetch)
1719 (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
1720 "superlu_dist_" version ".tar.gz"))
1721 (sha256
1722 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
29080870
EB		 1723 (modules '((guix build utils)))
1724 (snippet
1725 ;; Replace the non-free implementation of MC64 with a stub
1726 '(begin
1727 (use-modules (ice-9 regex)
1728 (ice-9 rdelim))
1729 (call-with-output-file "SRC/mc64ad.c"
1730 (lambda (port)
1731 (display "
1732#include <stdio.h>
1733#include <stdlib.h>
1734void mc64id_(int *a) {
1735 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1736 abort ();
1737}
1738void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
1739 int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
1740 fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
1741 abort ();
1742}\n" port)))
1743 (delete-file "SRC/mc64ad.f.bak")
1744 (substitute* "SRC/util.c" ;adjust default algorithm
1745 (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
1746 "RowPerm = NOROWPERM"))))
fc1adab1 1747 (patches (search-patches "superlu-dist-scotchmetis.patch"))))
a54aefea
EB		 1748 (build-system gnu-build-system)
1749 (native-inputs
1750 `(("tcsh" ,tcsh)))
1751 (inputs
19afbea1 1752 `(("gfortran" ,gfortran)))
a54aefea
EB		 1753 (propagated-inputs
1754 `(("openmpi" ,openmpi) ;headers include MPI heades
1755 ("lapack" ,lapack) ;required to link with output library
1756 ("pt-scotch" ,pt-scotch))) ;same
1757 (arguments
1758 `(#:parallel-build? #f ;race conditions using ar
1759 #:phases
1760 (alist-replace
1761 'configure
1762 (lambda* (#:key inputs outputs #:allow-other-keys)
1763 (call-with-output-file "make.inc"
1764 (lambda (port)
1765 (format port "
1766PLAT =
1767DSuperLUroot = ~a
1768DSUPERLULIB = ~a/lib/libsuperlu_dist.a
1769BLASDEF = -DUSE_VENDOR_BLAS
1770BLASLIB = -L~a/lib -lblas
1771PARMETISLIB = -L~a/lib \
1772 -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
1773 -lscotch -lscotcherr -lscotcherrexit
1774METISLIB = -L~:*~a/lib \
1775 -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
1776LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
1777ARCH = ar
1778ARCHFLAGS = cr
1779RANLIB = ranlib
1780CC = mpicc
1781PIC = -fPIC
1782CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
1783NOOPTS = -O0 -g $(PIC)
1784FORTRAN = mpifort
1785FFLAGS = -O2 -g $(PIC)
1786LOADER = $(CC)
1787CDEFS = -DAdd_"
1788 (getcwd)
1789 (assoc-ref outputs "out")
1790 (assoc-ref inputs "lapack")
1791 (assoc-ref inputs "pt-scotch")))))
1792 (alist-cons-after
1793 'unpack 'remove-broken-symlinks
1794 (lambda _
1795 (for-each delete-file
1796 (find-files "MAKE_INC" "\\.#make\\..*")))
1797 (alist-cons-before
1798 'build 'create-install-directories
1799 (lambda* (#:key outputs #:allow-other-keys)
1800 (for-each
1801 (lambda (dir)
1802 (mkdir-p (string-append (assoc-ref outputs "out")
1803 "/" dir)))
1804 '("lib" "include")))
1805 (alist-replace
1806 'check
1807 (lambda _
1808 (with-directory-excursion "EXAMPLE"
1809 (and
1810 (zero? (system* "mpirun" "-n" "2"
1811 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
1812 (zero? (system* "mpirun" "-n" "2"
1813 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
1814 (alist-replace
1815 'install
1816 (lambda* (#:key outputs #:allow-other-keys)
1817 ;; Library is placed in lib during the build phase. Copy over
1818 ;; headers to include.
1819 (let* ((out (assoc-ref outputs "out"))
1820 (incdir (string-append out "/include")))
1821 (for-each (lambda (file)
1822 (let ((base (basename file)))
1823 (format #t "installing `~a' to `~a'~%"
1824 base incdir)
1825 (copy-file file
1826 (string-append incdir "/" base))))
1827 (find-files "SRC" ".*\\.h$"))))
1828 %standard-phases)))))))
1829 (home-page (package-home-page superlu))
1830 (synopsis "Parallel supernodal direct solver")
1831 (description
1832 "SuperLU_DIST is a parallel extension to the serial SuperLU library.
1833It is targeted for distributed memory parallel machines. SuperLU_DIST is
1834implemented in ANSI C, and MPI for communications.")
1835 (license license:bsd-3)))
1836
f8ed036a
EB		 1837(define-public scotch
1838 (package
1839 (name "scotch")
6c798540 1840 (version "6.0.4")
f8ed036a
EB		 1841 (source
1842 (origin
1843 (method url-fetch)
6c798540 1844 (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
f8ed036a
EB		 1845 "scotch_" version ".tar.gz"))
1846 (sha256
6c798540 1847 (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
fc1adab1
AK		 1848 (patches (search-patches "scotch-test-threading.patch"
1849 "pt-scotch-build-parallelism.patch"))))
f8ed036a
EB		 1850 (build-system gnu-build-system)
1851 (inputs
1852 `(("zlib" ,zlib)
d5ceeb5a 1853 ("flex" ,flex-2.6.1) ; A bug in flex prevents building with flex-2.6.3.
f8ed036a
EB		 1854 ("bison" ,bison)))
1855 (arguments
1856 `(#:phases
d6602ee9
EB		 1857 (modify-phases %standard-phases
1858 (add-after
1859 'unpack 'chdir-to-src
1860 (lambda _ (chdir "src")))
1861 (replace
1862 'configure
1863 (lambda _
1864 (call-with-output-file "Makefile.inc"
1865 (lambda (port)
1866 (format port "
f8ed036a
EB		 1867EXE =
1868LIB = .a
1869OBJ = .o
1870MAKE = make
1871AR = ar
1872ARFLAGS = -ruv
cf0ec6c4 1873CAT = cat
f8ed036a
EB		 1874CCS = gcc
1875CCP = mpicc
1876CCD = gcc
1877CPPFLAGS =~{ -D~a~}
6c798540 1878CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
f8ed036a
EB		 1879LDFLAGS = -lz -lm -lrt -lpthread
1880CP = cp
1881LEX = flex -Pscotchyy -olex.yy.c
1882LN = ln
1883MKDIR = mkdir
1884MV = mv
1885RANLIB = ranlib
1886YACC = bison -pscotchyy -y -b y
1887"
d6602ee9
EB		 1888 '("COMMON_FILE_COMPRESS_GZ"
1889 "COMMON_PTHREAD"
1890 "COMMON_RANDOM_FIXED_SEED"
26599d69 1891 "INTSIZE64" ;use 'long' instead of 'int'
cf0ec6c4
EB		 1892 ;; Prevents symbolc clashes with libesmumps
1893 "SCOTCH_RENAME"
d6602ee9
EB		 1894 ;; XXX: Causes invalid frees in superlu-dist tests
1895 ;; "SCOTCH_PTHREAD"
1896 ;; "SCOTCH_PTHREAD_NUMBER=2"
1897 "restrict=__restrict"))))))
cf0ec6c4
EB		 1898 (add-after
1899 'build 'build-esmumps
1900 (lambda _
1901 (zero? (system* "make"
1902 (format #f "-j~a" (parallel-job-count))
1903 "esmumps"))))
d6602ee9 1904 (replace
f8ed036a
EB		 1905 'install
1906 (lambda* (#:key outputs #:allow-other-keys)
1907 (let ((out (assoc-ref outputs "out")))
1908 (mkdir out)
1909 (zero? (system* "make"
1910 (string-append "prefix=" out)
cf0ec6c4
EB		 1911 "install"))
1912 ;; esmumps files are not installed with the above
1913 (for-each (lambda (f)
1914 (copy-file f (string-append out "/include/" f)))
1915 (find-files "../include" ".*esmumps.h$"))
1916 (for-each (lambda (f)
1917 (copy-file f (string-append out "/lib/" f)))
1918 (find-files "../lib" "^lib.*esmumps.*"))))))))
f8ed036a
EB		 1919 (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
1920 (synopsis "Programs and libraries for graph algorithms")
1921 (description "SCOTCH is a set of programs and libraries which implement
1922the static mapping and sparse matrix reordering algorithms developed within
1923the SCOTCH project. Its purpose is to apply graph theory, with a divide and
1924conquer approach, to scientific computing problems such as graph and mesh
1925partitioning, static mapping, and sparse matrix ordering, in application
1926domains ranging from structural mechanics to operating systems or
1927bio-chemistry.")
1928 ;; See LICENSE_en.txt
1929 (license license:cecill-c)))
6acb4adb
EB		 1930
1931(define-public pt-scotch
1932 (package (inherit scotch)
1933 (name "pt-scotch")
1934 (propagated-inputs
1935 `(("openmpi" ,openmpi))) ;Headers include MPI headers
1936 (arguments
1937 (substitute-keyword-arguments (package-arguments scotch)
1938 ((#:phases scotch-phases)
d6602ee9
EB		 1939 `(modify-phases ,scotch-phases
1940 (replace
1941 'build
d6602ee9
EB		 1942 (lambda _
1943 (and
cf0ec6c4
EB		 1944 (zero? (system* "make"
1945 (format #f "-j~a" (parallel-job-count))
1946 "ptscotch" "ptesmumps"))
d6602ee9
EB		 1947 ;; Install the serial metis compatibility library
1948 (zero? (system* "make" "-C" "libscotchmetis" "install")))))
1949 (replace
1950 'check
1951 (lambda _ (zero? (system* "make" "ptcheck"))))))))
6acb4adb 1952 (synopsis "Programs and libraries for graph algorithms (with MPI)")))
5698b8b8 1953
aa75ad00
EB		 1954(define-public metis
1955 (package
1956 (name "metis")
1957 (version "5.1.0")
1958 (source
1959 (origin
1960 (method url-fetch)
1961 (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
1962 "metis-" version ".tar.gz"))
1963 (sha256
1964 (base32
1965 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
1966 (build-system cmake-build-system)
1967 (inputs
1968 `(("blas" ,openblas)))
1969 (arguments
1970 `(#:tests? #f ;no tests
1971 #:configure-flags `("-DSHARED=ON"
1972 ,(string-append "-DGKLIB_PATH=" (getcwd)
1973 "/metis-" ,version "/GKlib"))))
1974 (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
1975 (synopsis "Graph partitioning and fill-reducing matrix ordering library")
1976 (description
1977 "METIS is a set of serial programs for partitioning graphs, partitioning
1978finite element meshes, and producing fill-reducing orderings for sparse
1979matrices. The algorithms implemented in METIS are based on the multilevel
1980recursive-bisection, multilevel k-way, and multi-constraint partitioning
1981schemes.")
1982 (license license:asl2.0))) ;As of version 5.0.3
1983
700ff222
EB		 1984(define-public p4est
1985 (package
1986 (name "p4est")
1987 (version "1.1")
1988 (source
1989 (origin
1990 (method url-fetch)
1991 (uri (string-append "http://p4est.github.io/release/p4est-"
1992 version ".tar.gz"))
1993 (sha256
1994 (base32
1995 "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb"))))
1996 (build-system gnu-build-system)
1997 (inputs
1998 `(("fortran" ,gfortran)
1999 ("blas" ,openblas)
2000 ("lapack" ,lapack)
2001 ("zlib" ,zlib)))
2002 (arguments
2003 `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
2004 (assoc-ref %build-inputs "blas")
2005 " -lopenblas")
2006 ,(string-append "LAPACK_LIBS=-L"
2007 (assoc-ref %build-inputs "lapack")
2008 " -llapack"))))
2009 (home-page "http://www.p4est.org")
2010 (synopsis "Adaptive mesh refinement on forests of octrees")
2011 (description
2012 "The p4est software library enables the dynamic management of a
2013collection of adaptive octrees, conveniently called a forest of octrees.
2014p4est is designed to work in parallel and scales to hundreds of thousands of
2015processor cores.")
2016 (license license:gpl2+)))
2017
2018(define-public p4est-openmpi
2019 (package (inherit p4est)
2020 (name "p4est-openmpi")
2021 (inputs
2022 `(("mpi" ,openmpi)
2023 ,@(package-inputs p4est)))
2024 (arguments
2025 (substitute-keyword-arguments (package-arguments p4est)
2026 ((#:configure-flags cf)
2027 ``("--enable-mpi" ,@,cf))))
2028 (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
2029
5698b8b8
JD		 2030(define-public gsegrafix
2031 (package
2032 (name "gsegrafix")
2033 (version "1.0.6")
2034 (source
2035 (origin
2036 (method url-fetch)
2037 (uri (string-append "mirror://gnu/" name "/" name "-"
2038 version ".tar.gz"))
2039 (sha256
2040 (base32
2041 "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
2042 (build-system gnu-build-system)
2043 (arguments
2044 `(#:configure-flags '("LDFLAGS=-lm")))
2045 (inputs
2046 `(("libgnomecanvas" ,libgnomecanvas)
2047 ("libbonoboui" ,libbonoboui)
2048 ("libgnomeui" ,libgnomeui)
2049 ("libgnomeprintui" ,libgnomeprintui)
2050 ("popt" ,popt)))
2051 (native-inputs
2052 `(("pkg-config" ,pkg-config)))
6fd52309 2053 (home-page "https://www.gnu.org/software/gsegrafix/")
5698b8b8
JD		 2054 (synopsis "GNOME application to create scientific and engineering plots")
2055 (description "GSEGrafix is an application which produces high-quality graphical
2056plots for science and engineering. Plots are specified via simple ASCII
2057parameter files and data files and are presented in an anti-aliased GNOME
2058canvas. The program supports rectangular two-dimensional plots, histograms,
2059polar-axis plots and three-dimensional plots. Plots can be printed or saved
2060to BMP, JPEG or PNG image formats.")
2061 (license license:gpl3+)))
8731e527
JD		 2062
2063(define-public maxima
2064 (package
2065 (name "maxima")
89b8df97 2066 (version "5.40.0")
8731e527
JD		 2067 (source
2068 (origin
2069 (method url-fetch)
2070 (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
2071 version "-source/" name "-" version ".tar.gz"))
2072 (sha256
2073 (base32
89b8df97 2074 "15pp35ayglv723bjbqc60gcdv2bm54s6pywsm4i4cwbjsf64dzkl"))
fc1adab1 2075 (patches (search-patches "maxima-defsystem-mkdir.patch"))))
8731e527 2076 (build-system gnu-build-system)
df354a77 2077 (inputs
6b2eafaa 2078 `(("gcl" ,gcl)
df354a77 2079 ("gnuplot" ,gnuplot) ;for plots
f36afe4d 2080 ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
df354a77
FB		 2081 (native-inputs
2082 `(("texinfo" ,texinfo)
ccbc5758
KK		 2083 ("perl" ,perl)
2084 ("python" ,python)))
8731e527 2085 (arguments
df354a77
FB		 2086 `(#:configure-flags
2087 (list "--enable-gcl"
2088 (string-append "--with-posix-shell="
2089 (assoc-ref %build-inputs "bash")
2090 "/bin/sh")
2091 (string-append "--with-wish="
2092 (assoc-ref %build-inputs "tk")
2093 "/bin/wish"
2094 (let ((v ,(package-version tk)))
2095 (string-take v (string-index-right v #\.)))))
df354a77 2096 ;; By default Maxima attempts to write temporary files to
77af7b24
MW		 2097 ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
2098 ;; Work around that.
df354a77 2099 #:make-flags (list "TMPDIR=/tmp")
6b2eafaa
KK		 2100 #:phases (alist-cons-before
2101 'check 'pre-check
2102 (lambda _
2103 (chmod "src/maxima" #o555))
2104 ;; Make sure the doc and emacs files are found in the
2105 ;; standard location. Also configure maxima to find gnuplot
2106 ;; without having it on the PATH.
2107 (alist-cons-after
2108 'install 'post-install
2109 (lambda* (#:key outputs inputs #:allow-other-keys)
2110 (let* ((gnuplot (assoc-ref inputs "gnuplot"))
2111 (out (assoc-ref outputs "out"))
2112 (datadir (string-append out "/share/maxima/" ,version)))
2113 (with-directory-excursion out
2114 (mkdir-p "share/emacs")
2115 (mkdir-p "share/doc")
2116 (symlink
2117 (string-append datadir "/emacs/")
2118 (string-append out "/share/emacs/site-lisp"))
2119 (symlink
2120 (string-append datadir "/doc/")
2121 (string-append out "/share/doc/maxima"))
2122 (with-atomic-file-replacement
2123 (string-append datadir "/share/maxima-init.lisp")
2124 (lambda (in out)
2125 (format out "~a ~s~a~%"
2126 "(setf $gnuplot_command "
2127 (string-append gnuplot "/bin/gnuplot") ")")
2128 (dump-port in out))))))
2129 %standard-phases))))
8731e527
JD		 2130 (home-page "http://maxima.sourceforge.net")
2131 (synopsis "Numeric and symbolic expression manipulation")
2132 (description "Maxima is a system for the manipulation of symbolic and
2133numerical expressions. It yields high precision numeric results by using
2134exact fractions, arbitrary precision integers, and variable precision floating
e881752c 2135point numbers.")
8731e527
JD		 2136 ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
2137 ;; Others simply say "GNU General Public License" without stating a
2138 ;; version (which implicitly means gpl1+).
2139 ;; At least one file (src/maxima.asd) says "version 2."
2140 ;; GPLv2 only is therefore the smallest subset.
f36afe4d 2141 (license license:gpl2)))
ec322be2 2142
9aafbc0c
MW		 2143(define-public wxmaxima
2144 (package
2145 (name "wxmaxima")
5143517c 2146 (version "17.05.0")
9aafbc0c
MW		 2147 (source
2148 (origin
2149 (method url-fetch)
5143517c
KK		 2150 (uri (string-append "https://github.com/andrejv/" name "/archive"
2151 "/Version-" version ".tar.gz"))
2152 (file-name (string-append name "-" version ".tar.gz"))
9aafbc0c
MW		 2153 (sha256
2154 (base32
5143517c 2155 "1bsyd7r12xm2crpizb9iyyki3j0mbazzzwbsh871m06dv2wk97gq"))))
9aafbc0c 2156 (build-system gnu-build-system)
5143517c
KK		 2157 (native-inputs
2158 `(("autoconf" ,autoconf)
2159 ("automake" ,automake)
2160 ("gettext" ,gettext-minimal)))
9aafbc0c
MW		 2161 (inputs
2162 `(("wxwidgets" ,wxwidgets)
de477809
SB		 2163 ("maxima" ,maxima)
2164 ;; Runtime support.
2165 ("adwaita-icon-theme" ,adwaita-icon-theme)
2166 ("gtk+" ,gtk+)
2167 ("shared-mime-info" ,shared-mime-info)))
9aafbc0c
MW		 2168 (arguments
2169 `(#:phases (modify-phases %standard-phases
5143517c
KK		 2170 (add-before
2171 'configure 'autoconf
2172 (lambda _
2173 (zero? (system* "./bootstrap"))))
9aafbc0c
MW		 2174 (add-after
2175 'install 'wrap-program
2176 (lambda* (#:key inputs outputs #:allow-other-keys)
2177 (wrap-program (string-append (assoc-ref outputs "out")
2178 "/bin/wxmaxima")
2179 `("PATH" ":" prefix
2180 (,(string-append (assoc-ref inputs "maxima")
de477809
SB		 2181 "/bin")))
2182 ;; For GtkFileChooserDialog.
2183 `("GSETTINGS_SCHEMA_DIR" =
2184 (,(string-append (assoc-ref inputs "gtk+")
2185 "/share/glib-2.0/schemas")))
2186 `("XDG_DATA_DIRS" ":" prefix
2187 (;; Needed by gdk-pixbuf to know supported icon formats.
2188 ,(string-append
2189 (assoc-ref inputs "shared-mime-info") "/share")
2190 ;; The default icon theme of GTK+.
2191 ,(string-append
2192 (assoc-ref inputs "adwaita-icon-theme") "/share"))))
9aafbc0c
MW		 2193 #t)))))
2194 (home-page "https://andrejv.github.io/wxmaxima/")
2195 (synopsis "Graphical user interface for the Maxima computer algebra system")
2196 (description
2197 "wxMaxima is a graphical user interface for the Maxima computer algebra
2198system. It eases the use of Maxima by making most of its commands available
2199through a menu system and by providing input dialogs for commands that require
2200more than one argument. It also implements its own display engine that
2201outputs mathematical symbols directly instead of depicting them with ASCII
2202characters.
2203
2204wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
2205text and mathematical calculations to create documents, exporting of input and
2206output to TeX, and a browser for Maxima's manual including command index and
2207full text searching.")
2208 (license license:gpl2+)))
2209
b15e47f9
RW		 2210(define-public armadillo
2211 (package
2212 (name "armadillo")
133cba8c 2213 (version "7.800.2")
b15e47f9
RW		 2214 (source (origin
2215 (method url-fetch)
2216 (uri (string-append "mirror://sourceforge/arma/armadillo-"
7397cd9e 2217 version ".tar.xz"))
b15e47f9
RW		 2218 (sha256
2219 (base32
133cba8c 2220 "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
b15e47f9
RW		 2221 (build-system cmake-build-system)
2222 (arguments `(#:tests? #f)) ;no test target
2223 (inputs
2224 `(("openblas" ,openblas)
2225 ("lapack" ,lapack)
2226 ("arpack" ,arpack-ng)))
2227 (home-page "http://arma.sourceforge.net/")
2228 (synopsis "C++ linear algebra library")
2229 (description
2230 "Armadillo is a C++ linear algebra library, aiming towards a good balance
2231between speed and ease of use. It is useful for algorithm development
2232directly in C++, or quick conversion of research code into production
2233environments. It can be used for machine learning, pattern recognition,
2234signal processing, bioinformatics, statistics, econometrics, etc. The library
2235provides efficient classes for vectors, matrices and cubes, as well as 150+
2236associated functions (eg. contiguous and non-contiguous submatrix views).")
fe418cc5 2237 (license license:asl2.0)))
b15e47f9 2238
279663ef 2239(define-public muparser
d7cff656
LF		 2240 ;; When switching download sites, muparser re-issued a 2.2.5 release with a
2241 ;; different hash. In order to make `guix package --upgrade` work correctly,
2242 ;; we set a Guix packaging revision.
2243 ;; When the next version of muparser is released, we can remove
2244 ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
2245 (let ((upstream-version "2.2.5")
2246 (revision "2"))
2247 (package
2248 (name "muparser")
2249 (version (string-append upstream-version "-" revision))
2250 (source
2251 (origin
2252 (method url-fetch)
2253 (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
2254 upstream-version ".tar.gz"))
2255 (file-name (string-append name "-" version ".tar.gz"))
2256 (sha256
2257 (base32
2258 "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
2259 (build-system gnu-build-system)
2260 (arguments
2261 `(#:configure-flags '("--enable-samples=no")
2262 #:tests? #f)) ;no "check" target
2263 (home-page "http://muparser.beltoforion.de/")
2264 (synopsis "Fast parser library for mathematical expressions")
2265 (description
2266 "muParser is an extensible high performance math parser library. It is
2267based on transforming an expression into a bytecode and precalculating constant
2268parts of it.")
2269 (license license:expat))))
279663ef 2270
e73b49fb
RW		 2271(define-public openblas
2272 (package
2273 (name "openblas")
883d0a7d 2274 (version "0.2.19")
e73b49fb
RW		 2275 (source
2276 (origin
2277 (method url-fetch)
2278 (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
2279 version))
2280 (file-name (string-append name "-" version ".tar.gz"))
2281 (sha256
2282 (base32
883d0a7d 2283 "071zqnmnxhh0c9phzyn3f198yxa0hjxda7016azdbq2056sm70w7"))))
e73b49fb
RW		 2284 (build-system gnu-build-system)
2285 (arguments
5b5ea159 2286 `(#:tests? #f ;no "check" target
bd0b4379
RW		 2287 ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
2288 ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
2289 ;; we need to disable substitutions.
71923a91
AE		 2290 #:substitutable?
2291 ,(let ((system (or (%current-target-system) (%current-system))))
2292 (or (string-prefix? "x86_64" system)
bd0b4379 2293 (string-prefix? "i686" system)
83a34647
EF		 2294 (string-prefix? "mips" system)
2295 (string-prefix? "aarch64" system)))
e73b49fb
RW		 2296 #:make-flags
2297 (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
2298 "SHELL=bash"
af5b817e
RW		 2299 "NO_LAPACK=1"
2300 ;; Build the library for all supported CPUs. This allows
2301 ;; switching CPU targets at runtime with the environment variable
2302 ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
71923a91
AE		 2303 ;; Unfortunately, this is not supported on non-x86 architectures,
2304 ;; where it leads to failed builds.
2305 ,@(let ((system (or (%current-target-system) (%current-system))))
8a637e79
RW		 2306 (cond
2307 ((or (string-prefix? "x86_64" system)
71923a91 2308 (string-prefix? "i686" system))
8a637e79
RW		 2309 '("DYNAMIC_ARCH=1"))
2310 ;; On MIPS we force the "SICORTEX" TARGET, as for the other
2311 ;; two available MIPS targets special extended instructions
2312 ;; for Loongson cores are used.
2313 ((string-prefix? "mips" system)
2314 '("TARGET=SICORTEX"))
83a34647
EF		 2315 ;; On aarch64 force the generic 'armv8-a' target
2316 ((string-prefix? "aarch64" system)
2317 '("TARGET=ARMV8"))
8a637e79 2318 (else '()))))
e73b49fb
RW		 2319 ;; no configure script
2320 #:phases (alist-delete 'configure %standard-phases)))
2321 (inputs
19afbea1 2322 `(("fortran" ,gfortran)))
e73b49fb
RW		 2323 (native-inputs
2324 `(("cunit" ,cunit)
2325 ("perl" ,perl)))
2326 (home-page "http://www.openblas.net/")
2327 (synopsis "Optimized BLAS library based on GotoBLAS")
2328 (description
2329 "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
2330 (license license:bsd-3)))
2331
e1605e36
RW		 2332(define-public openlibm
2333 (package
2334 (name "openlibm")
26f6e565 2335 (version "0.5.1")
e1605e36
RW		 2336 (source
2337 (origin
2338 (method url-fetch)
2339 (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
2340 version ".tar.gz"))
2341 (file-name (string-append name "-" version ".tar.gz"))
2342 (sha256
2343 (base32
26f6e565 2344 "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
e1605e36
RW		 2345 (build-system gnu-build-system)
2346 (arguments
2347 `(#:make-flags
2348 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2349 #:phases
2350 ;; no configure script
2351 (alist-delete 'configure %standard-phases)
2352 #:tests? #f)) ;the tests are part of the default target
2353 (home-page "http://openlibm.org/")
2354 (synopsis "Portable C mathematical library (libm)")
2355 (description
2356 "OpenLibm is an effort to have a high quality, portable, standalone C
2357mathematical library (libm). It can be used standalone in applications and
2358programming language implementations. The project was born out of a need to
e881752c 2359have a good libm for the Julia programming language that worked consistently
e1605e36
RW		 2360across compilers and operating systems, and in 32-bit and 64-bit
2361environments.")
538c0e3b
EF		 2362 ;; Each architecture has its own make target, and there is none for mips.
2363 (supported-systems (delete "mips64el-linux" %supported-systems))
e1605e36
RW		 2364 ;; See LICENSE.md for details.
2365 (license (list license:expat
2366 license:isc
2367 license:bsd-2
2368 license:public-domain
2369 license:lgpl2.1+))))
2370
e62be58f
RW		 2371(define-public openspecfun
2372 (package
2373 (name "openspecfun")
49f54a74 2374 (version "0.5.2")
e62be58f
RW		 2375 (source
2376 (origin
2377 (method url-fetch)
2378 (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
2379 version ".tar.gz"))
2380 (file-name (string-append name "-" version ".tar.gz"))
2381 (sha256
2382 (base32
49f54a74 2383 "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
e62be58f
RW		 2384 (build-system gnu-build-system)
2385 (arguments
2386 '(#:tests? #f ;no "check" target
2387 #:make-flags
2388 (list (string-append "prefix=" (assoc-ref %outputs "out")))
2389 ;; no configure script
2390 #:phases (alist-delete 'configure %standard-phases)))
2391 (inputs
19afbea1 2392 `(("fortran" ,gfortran)))
e62be58f
RW		 2393 (home-page "https://github.com/JuliaLang/openspecfun")
2394 (synopsis "Collection of special mathematical functions")
2395 (description
2396 "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
2397portable package for Bessel Functions of a Complex Argument and Nonnegative
2398Order; it contains subroutines for computing Bessel functions and Airy
2399functions. Faddeeva allows computing the various error functions of arbitrary
2400complex arguments (Faddeeva function, error function, complementary error
2401function, scaled complementary error function, imaginary error function, and
2402Dawson function); given these, one can also easily compute Voigt functions,
2403Fresnel integrals, and similar related functions as well.")
2404 ;; Faddeeva is released under the Expat license; AMOS is included as
2405 ;; public domain software.
2406 (license (list license:expat license:public-domain))))
2407
2742f87e
RW		 2408(define-public suitesparse
2409 (package
2410 (name "suitesparse")
2411 (version "4.4.3")
2412 (source
2413 (origin
2414 (method url-fetch)
2415 (uri (string-append
2416 "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
2417 version ".tar.gz"))
2418 (sha256
2419 (base32
2420 "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
2421 (build-system gnu-build-system)
2422 (arguments
2423 '(#:parallel-build? #f ;cholmod build fails otherwise
2424 #:tests? #f ;no "check" target
2425 #:make-flags
2426 (list "CC=gcc"
2427 "BLAS=-lblas"
2428 "TBB=-ltbb"
2429 "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
2430 (string-append "INSTALL_LIB="
2431 (assoc-ref %outputs "out") "/lib")
2432 (string-append "INSTALL_INCLUDE="
2433 (assoc-ref %outputs "out") "/include"))
2434 #:phases
2435 (alist-cons-before
2436 'install 'prepare-out
2437 ;; README.txt states that the target directories must exist prior to
2438 ;; running "make install".
2439 (lambda _
2440 (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
2441 (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
2442 ;; no configure script
2443 (alist-delete 'configure %standard-phases))))
2444 (inputs
2445 `(("tbb" ,tbb)
2446 ("lapack" ,lapack)))
2447 (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
2448 (synopsis "Suite of sparse matrix software")
2449 (description
2450 "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
2451multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
2452multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
2453simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
2454CXSparse, a concise sparse Cholesky factorization package; and many other
2455packages.")
2456 ;; LGPLv2.1+:
2457 ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
2458 ;; GPLv2+:
2459 ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
2460 (license (list license:gpl2+ license:lgpl2.1+))))
2461
ec322be2
FB		 2462(define-public atlas
2463 (package
2464 (name "atlas")
3c98ac02 2465 (version "3.10.3")
ec322be2
FB		 2466 (source (origin
2467 (method url-fetch)
de67e922
LF		 2468 (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
2469 version "/atlas" version ".tar.bz2"))
ec322be2
FB		 2470 (sha256
2471 (base32
3c98ac02 2472 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
ec322be2
FB		 2473 (build-system gnu-build-system)
2474 (home-page "http://math-atlas.sourceforge.net/")
19afbea1 2475 (inputs `(("gfortran" ,gfortran)
ec322be2
FB		 2476 ("lapack-tar" ,(package-source lapack))))
2477 (outputs '("out" "doc"))
01480b9e
FB		 2478 ;; For the moment we drop support for MIPS at it fails to compile. See
2479 ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
2480 (supported-systems (delete "mips64el-linux" %supported-systems))
ec322be2
FB		 2481 (arguments
2482 `(#:parallel-build? #f
2483 #:parallel-tests? #f
f15615b1
LC		 2484
2485 ;; ATLAS tunes itself for the machine it is built on, as explained at
2486 ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
2487 ;; For this reason, we want users to build it locally instead of using
2488 ;; substitutes.
2489 #:substitutable? #f
2490
ec322be2
FB		 2491 #:modules ((srfi srfi-26)
2492 (srfi srfi-1)
2493 (guix build gnu-build-system)
2494 (guix build utils))
40029cbe 2495 #:configure-flags
ec322be2
FB		 2496 `(;; Generate position independent code suitable for dynamic libraries
2497 ;; and use WALL timer to get more accurate timing.
2498 "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
2499 ;; Set word width.
2500 "-b"
2501 ,,(if (string-match "64" (%current-system))
2502 "64"
2503 "32")
2504 ;; Disable parallel build as it gives errors: atlas_pthread.h is
2505 ;; needed to compile C files before it is generated.
2506 "-Ss" "pmake" "make -j 1"
af89a667
FB		 2507 ;; Probe is failing for MIPS. We therefore define the system
2508 ;; architecture explicitly by setting (-A) MACHINETYPE = 49
2509 ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
2510 ,,@(if (string-prefix? "mips" (%current-system))
2511 (list "-A" "49" "-V" "1")
2512 (list))
ec322be2
FB		 2513 ;; Generate shared libraries.
2514 "--shared"
2515 ;; Build a full LAPACK library.
2516 ,(string-append "--with-netlib-lapack-tarfile="
2517 (assoc-ref %build-inputs "lapack-tar")))
2518 #:phases
e5b4b96b
EF		 2519 (modify-phases %standard-phases
2520 (add-after 'install 'install-doc
2521 (lambda* (#:key outputs inputs #:allow-other-keys)
2522 (let ((doc (string-append (assoc-ref outputs "doc")
2523 "/share/doc/atlas")))
2524 (mkdir-p doc)
2525 (fold (lambda (file previous)
2526 (and previous (zero? (system* "cp" file doc))))
2527 #t (find-files "../ATLAS/doc" ".*")))))
2528 (add-after 'check 'check-pt
2529 (lambda _ (zero? (system* "make" "ptcheck"))))
2530 ;; Fix files required to run configure.
2531 (add-before 'configure 'fix-/bin/sh
ec322be2
FB		 2532 (lambda _
2533 ;; Use `sh', not `/bin/sh'.
2534 (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
2535 (("/bin/sh")
e5b4b96b
EF		 2536 "sh"))))
2537 ;; Fix /bin/sh in generated make files.
2538 (add-after 'configure 'fix-/bin/sh-in-generated-files
2539 (lambda _
2540 (substitute* (find-files "." "^[Mm]ake\\.inc.*")
2541 (("/bin/sh")
2542 "sh"))))
2543 ;; ATLAS configure program does not accepts the default flags
2544 ;; passed by the 'gnu-build-system'.
2545 (replace 'configure
2546 (lambda* (#:key native-inputs inputs outputs
2547 (configure-flags '())
2548 #:allow-other-keys #:rest args)
2549 (let* ((prefix (assoc-ref outputs "out"))
2550 (bash (or (and=> (assoc-ref
2551 (or native-inputs inputs) "bash")
2552 (cut string-append <> "/bin/bash"))
2553 "/bin/sh"))
2554 (flags `(,(string-append "--prefix=" prefix)
2555 ,@configure-flags))
2556 (abs-srcdir (getcwd))
2557 (srcdir (string-append "../" (basename abs-srcdir))))
2558 (format #t "source directory: ~s (relative from build: ~s)~%"
2559 abs-srcdir srcdir)
2560 (mkdir "../build")
2561 (chdir "../build")
2562 (format #t "build directory: ~s~%" (getcwd))
2563 (format #t "configure flags: ~s~%" flags)
2564 (zero? (apply system* bash
2565 (string-append srcdir "/configure")
2566 flags))))))))
ec322be2
FB		 2567 (synopsis "Automatically Tuned Linear Algebra Software")
2568 (description
2569 "ATLAS is an automatically tuned linear algebra software library
2570providing C and Fortran77 interfaces to a portably efficient BLAS
2571implementation, as well as a few routines from LAPACK.
2572
f15615b1
LC		 2573Optimization occurs at build time. For this reason, the library is built on
2574the machine where it is installed, without resorting to pre-built substitutes.
ec322be2 2575
f15615b1 2576Before building the library, CPU throttling should be disabled. This can be
d97c429a 2577done in the BIOS, or, on GNU/Linux, with the following command:
ec322be2 2578
8e9ba611 2579@example
d97c429a 2580# cpupower --governor performance
8e9ba611 2581@end example
ec322be2 2582
d97c429a 2583Failure to do so will result in a library with poor performance.")
ec322be2 2584 (license license:bsd-3)))
c12efc72
AE		 2585
2586(define-public glm
2587 (package
2588 (name "glm")
2589 (version "0.9.6.3")
2590 (source
2591 (origin
2592 (method url-fetch)
de67e922
LF		 2593 (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
2594 "/glm-" version ".zip"))
c12efc72
AE		 2595 (sha256
2596 (base32
2597 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
2598 (build-system cmake-build-system)
2599 (native-inputs
2600 `(("unzip" ,unzip)))
2601 (home-page "http://glm.g-truc.net")
2602 (synopsis "OpenGL Mathematics library")
2603 (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
2604library for graphics software based on the OpenGL Shading Language (GLSL)
2605specifications.")
2606 (license license:expat)))
7f18257b
AE		 2607
2608(define-public lpsolve
2609 (package
2610 (name "lpsolve")
2611 (version "5.5.2.0")
2612 (source
2613 (origin
2614 (method url-fetch)
2615 (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
2616 "/lp_solve_" version "_source.tar.gz"))
2617 (sha256
2618 (base32
2619 "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
2620 (modules '((guix build utils)))
2621 (snippet
2622 '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
2623 (("^c=cc") "c=gcc")
2624 ;; Pretend to be on a 64 bit platform to obtain a common directory
2625 ;; name for the build results on all architectures; nothing else
2626 ;; seems to depend on it.
5dbfbef7
LC		 2627 (("^PLATFORM=.*$") "PLATFORM=ux64\n")
2628
2629 ;; The check for 'isnan' as it is written fails with
2630 ;; "non-floating-point argument in call to function
2631 ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
2632 ;; definition, which in turn leads to bad things. Fix the feature
2633 ;; test.
2634 (("isnan\\(0\\)") "isnan(0.)")))))
7f18257b
AE		 2635 (build-system gnu-build-system)
2636 (arguments
2637 `(#:tests? #f ; no check target
2638 #:phases
2639 (modify-phases %standard-phases
2640 (delete 'configure)
2641 (replace 'build
2642 (lambda _
6689d094
LC		 2643 (and (with-directory-excursion "lpsolve55"
2644 (zero? (system* "bash" "ccc")))
2645 (with-directory-excursion "lp_solve"
2646 (zero? (system* "bash" "ccc"))))))
7f18257b
AE		 2647 (replace 'install
2648 (lambda* (#:key outputs #:allow-other-keys)
2649 (let* ((out (assoc-ref outputs "out"))
2650 (bin (string-append out "/bin"))
2651 (lib (string-append out "/lib"))
2652 ;; This is where LibreOffice expects to find the header
2653 ;; files, and where they are installed by Debian.
2654 (include (string-append out "/include/lpsolve")))
2655 (mkdir-p lib)
2656 (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
2657 (string-append lib "/liblpsolve55.a"))
2658 (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
2659 (string-append lib "/liblpsolve55.so"))
96c46210
LC		 2660 (install-file "lp_solve/bin/ux64/lp_solve" bin)
2661
7f18257b
AE		 2662 ;; Install a subset of the header files as on Debian
2663 ;; (plus lp_bit.h, which matches the regular expression).
96c46210
LC		 2664 (for-each (lambda (name)
2665 (install-file name include))
2666 (find-files "." "lp_[HMSa-z].*\\.h$"))
7f18257b 2667 (with-directory-excursion "shared"
96c46210
LC		 2668 (for-each (lambda (name)
2669 (install-file name include))
2670 (find-files "." "\\.h$")))
7f18257b
AE		 2671 #t))))))
2672 (home-page "http://lpsolve.sourceforge.net/")
2673 (synopsis "Mixed integer linear programming (MILP) solver")
2674 (description
2675 "lp_solve is a mixed integer linear programming solver based on the
2676revised simplex and the branch-and-bound methods.")
2677 (license license:lgpl2.1+)))
a17d4564
EB		 2678
2679(define-public dealii
2680 (package
2681 (name "dealii")
101e8472 2682 (version "8.4.1")
a17d4564
EB		 2683 (source
2684 (origin
2685 (method url-fetch)
2686 (uri (string-append "https://github.com/dealii/dealii/releases/"
2687 "download/v" version "/dealii-" version ".tar.gz"))
2688 (sha256
2689 (base32
101e8472 2690 "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
a17d4564
EB		 2691 (modules '((guix build utils)))
2692 (snippet
2693 ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
2694 '(delete-file-recursively "bundled"))))
2695 (build-system cmake-build-system)
2696 (inputs
2697 `(("tbb" ,tbb)
2698 ("zlib" ,zlib)
2699 ("boost" ,boost)
2700 ("p4est" ,p4est)
2701 ("blas" ,openblas)
2702 ("lapack" ,lapack)
2703 ("arpack" ,arpack-ng)
2704 ("muparser" ,muparser)
2705 ("gfortran" ,gfortran)
2706 ("suitesparse" ,suitesparse))) ;for UMFPACK
2707 (arguments
2708 `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
2709 #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
2710 #:phases (modify-phases %standard-phases
2711 (add-after
2712 'install 'hint-example-prefix
2713 ;; Set Cmake hints in examples so that they can find this
2714 ;; deal.II when configuring.
2715 (lambda* (#:key outputs #:allow-other-keys)
2716 (let* ((out (assoc-ref %outputs "out"))
2717 (exmpl (string-append out "/share/doc"
2718 "/dealii/examples")))
2719 (substitute* (find-files exmpl "CMakeLists.txt")
2720 (("([[:space:]]*HINTS.*)\n" _ line)
2721 (string-append line " $ENV{HOME}/.guix-profile "
2722 out "\n")))
2723 #t))))))
2724 (home-page "https://www.dealii.org")
2725 (synopsis "Finite element library")
2726 (description
2727 "Deal.II is a C++ program library targeted at the computational solution
2728of partial differential equations using adaptive finite elements. The main
2729aim of deal.II is to enable rapid development of modern finite element codes,
2730using among other aspects adaptive meshes and a wide array of tools often used
2731in finite element programs.")
2732 (license license:lgpl2.1+)))
2733
2734(define-public dealii-openmpi
2735 (package (inherit dealii)
2736 (name "dealii-openmpi")
2737 (inputs
2738 `(("mpi" ,openmpi)
2739 ;;Supported only with MPI:
2740 ("p4est" ,p4est-openmpi)
2741 ("petsc" ,petsc-openmpi)
2742 ("slepc" ,slepc-openmpi)
2743 ("metis" ,metis) ;for MUMPS
2744 ("scalapack" ,scalapack) ;for MUMPS
2745 ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
2746 ("arpack" ,arpack-ng-openmpi)
2747 ,@(fold alist-delete (package-inputs dealii)
2748 '("p4est" "arpack"))))
2749 (arguments
2750 (substitute-keyword-arguments (package-arguments dealii)
2751 ((#:configure-flags cf)
2752 ``("-DMPI_C_COMPILER=mpicc"
2753 "-DMPI_CXX_COMPILER=mpicxx"
2754 "-DMPI_Fortran_COMPILER=mpifort"
2755 ,@,cf))))
2756 (synopsis "Finite element library (with MPI support)")))
194c7f95
AE		 2757
2758(define-public flann
2759 (package
2760 (name "flann")
2761 (version "1.8.4")
2762 (source
2763 (origin
2764 (method url-fetch)
2765 (uri
2766 (string-append
2767 "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
2768 version "-src.zip"))
2769 (sha256
2770 (base32
2771 "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
2772 (build-system cmake-build-system)
6b6aca9b
LC		 2773 (outputs '("out"
2774 "octave")) ;46 MiB .mex file that pulls Octave
194c7f95
AE		 2775 (native-inputs
2776 `(("unzip" ,unzip)))
2777 (inputs
2778 `(("hdf5" ,hdf5)
2779 ("octave" ,octave)
2780 ("python" ,python-2) ; print syntax
2781 ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
2782 ("zlib" ,zlib)))
2783 (arguments
39b30337
LC		 2784 `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
2785 ;; taken 46 MiB unstripped, and 6 MiB stripped.
2786 #:strip-directories '("lib" "lib64" "libexec"
2787 "bin" "sbin" "share/flann/octave")
2788
9684e30b
LC		 2789 ;; Save 12 MiB by not installing .a files. Passing
2790 ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
2791 #:phases (modify-phases %standard-phases
6b6aca9b
LC		 2792 (add-before 'configure 'set-octave-directory
2793 (lambda* (#:key outputs #:allow-other-keys)
2794 ;; Install the .mex file in the "octave" output.
2795 (let ((out (assoc-ref outputs "octave")))
2796 (substitute* "src/matlab/CMakeLists.txt"
2797 (("share/flann/octave")
2798 (string-append out "/share/flann/octave")))
2799 #t)))
9684e30b
LC		 2800 (add-after 'install 'remove-static-libraries
2801 (lambda* (#:key outputs #:allow-other-keys)
2802 (let* ((out (assoc-ref outputs "out"))
2803 (lib (string-append out "/lib")))
2804 (for-each delete-file
2805 (find-files lib "\\.a$"))
2806 #t))))
2807
39b30337 2808 #:tests? #f)) ; The test data are downloaded from the Internet.
194c7f95
AE		 2809 (home-page "http://www.cs.ubc.ca/research/flann/")
2810 (synopsis "Library for approximate nearest neighbors computation")
2811 (description "FLANN is a library for performing fast approximate
2812nearest neighbor searches in high dimensional spaces. It implements a
2813collection of algorithms and a system for automatically choosing the best
2814algorithm and optimum parameters depending on the dataset.
2815
2816FLANN is written in C++ and contains bindings for C, Octave and Python.")
2817 (license (license:non-copyleft "file://COPYING"
2818 "See COPYING in the distribution."))))
d8c97beb
EF		 2819
2820(define-public wcalc
2821 (package
2822 (name "wcalc")
2823 (version "2.5")
2824 (source
2825 (origin
2826 (method url-fetch)
de67e922
LF		 2827 (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
2828 "wcalc-" version ".tar.bz2"))
d8c97beb
EF		 2829 (sha256
2830 (base32
2831 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
2832 (build-system gnu-build-system)
2833 (inputs
2834 `(("mpfr" ,mpfr)
2835 ("readline" ,readline)))
2836 (home-page "http://w-calc.sourceforge.net/index.php")
2837 (synopsis "Flexible command-line scientific calculator")
2838 (description "Wcalc is a very capable calculator. It has standard functions
2839(sin, asin, and sinh for example, in either radians or degrees), many
2840pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
2841variables, a command history, hex/octal/binary input and output, unit
2842conversions, embedded comments, and an expandable expression entry field. It
2843evaluates expressions using the standard order of operations.")
2844 (license license:gpl2+)))
45147b0c
FH		 2845
2846(define-public xaos
2847 (package
2848 (name "xaos")
2849 (version "3.6")
2850 (source (origin
2851 (method url-fetch)
de67e922
LF		 2852 (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
2853 "/xaos-" version ".tar.gz"))
45147b0c
FH		 2854 (sha256
2855 (base32
2856 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
2857 (build-system gnu-build-system)
b94a6ca0 2858 (native-inputs `(("gettext" ,gettext-minimal)))
45147b0c
FH		 2859 (inputs `(("libx11" ,libx11)
2860 ("zlib" ,zlib)
2861 ("libpng" ,libpng)
2862 ("gsl" ,gsl)))
2863 (arguments
2864 `(#:tests? #f ;no "check" target
2865 #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
2866 (synopsis "Real-time fractal zoomer")
2867 (description "GNU XaoS is a graphical program that generates fractal
2868patterns and allows you to zoom in and out of them infinitely in a fluid,
2869continuous manner. It also includes tutorials that help to explain how fractals
2870are built. It can generate many different fractal types such as the Mandelbrot
2871set.")
6fd52309 2872 (home-page "https://www.gnu.org/software/xaos/")
45147b0c 2873 (license license:gpl2+)))
528bb464
EB		 2874
2875(define-public hypre
2876 (package
2877 (name "hypre")
2878 (version "2.11.0")
2879 (source (origin
2880 (method url-fetch)
2881 (uri (string-append "https://github.com/LLNL/hypre/archive/"
2882 "v" version ".tar.gz"))
2883 (file-name (string-append name "-" version ".tar.gz"))
2884 (sha256
2885 (base32
2886 "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
2887 (modules '((guix build utils)))
2888 (snippet
2889 '(begin
2890 ;; Remove use of __DATE__ and __TIME__ for reproducibility;
2891 ;; substitute the tarball creation time.
2892 (substitute* "src/utilities/HYPRE_utilities.h"
2893 (("Date Compiled: .*$")
2894 "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
2895 #t))))
2896 (build-system gnu-build-system)
2897 (outputs '("out" ;6.1 MiB of headers and libraries
2898 "doc")) ;4.8 MiB of documentation
2899 (native-inputs
2900 `(("doc++" ,doc++)
2901 ("netpbm" ,netpbm)
2902 ("texlive" ,texlive) ;full package required for fonts
2903 ("ghostscript" ,ghostscript)))
2904 (inputs
2905 `(("blas" ,openblas)
2906 ("lapack" ,lapack)))
2907 (arguments
2908 `(#:modules ((srfi srfi-1)
2909 ,@%gnu-build-system-modules)
2910 #:configure-flags '("--enable-shared"
2911 "--disable-fortran"
2912 "--without-MPI"
2913 "--with-openmp"
2914 "--with-fei"
2915 "--with-lapack"
2916 "--with-blas")
2917 #:phases
2918 (modify-phases %standard-phases
2919 (add-before 'configure 'chdir-src
2920 (lambda _ (chdir "src")))
2921 (replace 'configure
2922 (lambda* (#:key build target configure-flags
2923 #:allow-other-keys #:rest args)
2924 (let* ((configure (assoc-ref %standard-phases 'configure)))
2925 (apply configure
2926 (append args
2927 (list #:configure-flags
2928 (cons (string-append
2929 "--host=" (or target build))
2930 configure-flags)))))))
2931 (add-after 'build 'build-docs
2932 (lambda _
2933 (zero? (system* "make" "-Cdocs" "pdf" "html"))))
2934 (replace 'check
2935 (lambda _
2936 (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
2937 (setenv "PATH" (string-append "." ":" (getenv "PATH")))
2938 (and (system* "make" "check" "CHECKRUN=")
2939 (fold (lambda (filename result)
2940 (and result
2941 (let ((size (stat:size (stat filename))))
2942 (when (not (zero? size))
2943 (format #t "~a size ~d; error indication~%"
2944 filename size))
2945 (zero? size))))
2946 #t
2947 (find-files "test" ".*\\.err$")))))
2948 (add-after 'install 'install-docs
2949 (lambda* (#:key outputs #:allow-other-keys)
2950 ;; Custom install because docs/Makefile doesn't honor ${docdir}.
2951 (let* ((doc (assoc-ref outputs "doc"))
2952 (docdir (string-append doc "/share/doc/hypre-" ,version)))
528bb464
EB		 2953 (with-directory-excursion "docs"
2954 (for-each (lambda (base)
2955 (install-file (string-append base ".pdf") docdir)
2956 (copy-recursively base docdir)) ;html docs
2957 '("HYPRE_usr_manual"
2958 "HYPRE_ref_manual")))
2959 #t))))))
2960 (home-page "http://www.llnl.gov/casc/hypre/")
2961 (synopsis "Library of solvers and preconditioners for linear equations")
2962 (description
2963 "HYPRE is a software library of high performance preconditioners and
2964solvers for the solution of large, sparse linear systems of equations. It
2965features multigrid solvers for both structured and unstructured grid
2966problems.")
2967 (license license:lgpl2.1)))
2968
2969(define-public hypre-openmpi
2970 (package (inherit hypre)
2971 (name "hypre-openmpi")
2972 (inputs
2973 `(("mpi" ,openmpi)
2974 ,@(package-inputs hypre)))
2975 (arguments
2976 (substitute-keyword-arguments (package-arguments hypre)
2977 ((#:configure-flags flags)
2978 ``("--with-MPI"
2979 ,@(delete "--without-MPI" ,flags)))))
2980 (synopsis "Parallel solvers and preconditioners for linear equations")
2981 (description
2982 "HYPRE is a software library of high performance preconditioners and
2983solvers for the solution of large, sparse linear systems of equations on
2984parallel computers. It features parallel multigrid solvers for both
2985structured and unstructured grid problems.")))
6c90e183
EB		 2986
2987(define-public matio
2988 (package
2989 (name "matio")
2990 (version "1.5.6")
2991 (source
2992 (origin
2993 (method url-fetch)
de67e922 2994 (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
6c90e183
EB		 2995 "matio-" version ".tar.gz"))
2996 (sha256
2997 (base32
2998 "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
2999 (build-system gnu-build-system)
3000 (inputs
3001 `(("zlib" ,zlib)
3002 ("hdf5" ,hdf5)))
3003 (home-page "http://matio.sourceforge.net/")
3004 (synopsis "Library for reading and writing MAT files")
3005 (description "Matio is a library for reading and writing MAT files. It
3006supports compressed MAT files, as well as newer (version 7.3) MAT files.")
3007 (license license:bsd-2)))
d721c83a
EB		 3008
3009(define-public libhilbert
3010 (package
3011 (name "libhilbert")
3012 (version "0.2-1")
3013 (source
3014 (origin
3015 (method url-fetch)
3016 (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
3017 "libhilbert-" version ".tar.gz"))
3018 (sha256
3019 (base32
3020 "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
3021 (build-system gnu-build-system)
3022 (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
3023 (synopsis "Hilbert indices for multidimensional data")
3024 (description "The libhilbert library can efficiently calculate Hilbert
3025curves and order-preserving representations of Hilbert curve indices that use
3026the same amount of space as the original point representation. This is useful
3027when using the Gilbert curve as a space filling curve through a
3028high-dimensional space where not all demensions have the same cardinality.")
3029 (license license:lgpl2.1+)))
517318ad
LF		 3030
3031(define-public vc
3032 (package
3033 (name "vc")
3034 (version "1.2.0")
3035 (source
3036 (origin (method url-fetch)
3037 (uri (string-append "https://github.com/VcDevel/Vc/releases/"
3038 "download/" version "/Vc-" version ".tar.gz"))
3039 (sha256
3040 (base32
3041 "1rh6dhqar3y07n4xqyml0sa0v48qv3ch9dc3yc2in855hlh4vnqi"))))
3042 (build-system cmake-build-system)
3043 (arguments
3044 '(#:configure-flags
3045 '("-DBUILD_TESTING=ON")))
3046 (synopsis "SIMD vector classes for C++")
3047 (description "Vc provides portable, zero-overhead C++ types for explicitly
3048data-parallel programming. It is a library designed to ease explicit
3049vectorization of C++ code. Its types enable explicitly stating data-parallel
3050operations on multiple values. The parallelism is therefore added via the type
3051system. Vc has an intuitive API and provides portability between different
3052compilers and compiler versions as well as portability between different vector
3053instruction sets. Thus, an application written with Vc can be compiled for:
3054@enumerate
3055@item AVX and AVX2
d1e4ad1b 3056@item SSE2 up to SSE4.2 or SSE4a
517318ad
LF		 3057@item Scalar
3058@item MIC
3059@item NEON (in development)
3060@item NVIDIA GPUs / CUDA (in development)
3061@end enumerate\n")
3062 (home-page "https://github.com/VcDevel/Vc")
3063 (license license:bsd-3)))
54052a54 3064
3065(define-public reducelcs
3066 ;; This is the last commit which is available upstream, no
3067 ;; release happened since 2010.
3068 (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
3069 (revision "1"))
3070 (package
3071 (name "reducelcs")
3072 (version (string-append "1.0-" revision "." (string-take commit 7)))
3073 (source
3074 (origin
3075 (method git-fetch)
3076 (uri (git-reference
3077 (url "https://github.com/gdv/Reduce-Expand-for-LCS")
3078 (commit commit)))
3079 (file-name (string-append name "-" version "-checkout"))
3080 (sha256
3081 (base32
3082 "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
3083 (build-system gnu-build-system)
3084 (inputs
3085 `(("openlibm" ,openlibm)))
3086 (arguments
3087 `(#:tests? #f ; no tests
3088 #:phases
3089 (modify-phases %standard-phases
3090 (delete 'configure) ; No configure script exists.
3091 (replace 'install ; No install phase exists.
3092 (lambda* (#:key outputs #:allow-other-keys)
3093 (let* ((out (assoc-ref outputs "out"))
3094 (bin (string-append out "/bin")))
3095 (install-file "Approximation" bin)
3096 (install-file "CollectResults" bin)
3097 (install-file "GenerateInstances" bin)
3098 #t))))))
3099 (synopsis "Approximate Longest Commons Subsequence computation tool")
3100 (description
3101 "@code{reduceLCS} is an implementation of the Reduce-Expand
3102algorithm for LCS. It is a fast program to compute the approximate
3103Longest Commons Subsequence of a set of strings.")
3104 (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
c000b6b1 3105 (license license:gpl3+))))
479c4273
JD		 3106
3107(define-public jacal
3108 (package
3109 (name "jacal")
3110 (version "1c4")
3111 (source (origin
3112 (method url-fetch)
3113 (uri (string-append
3114 "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
3115 version ".zip"))
3116 (sha256 (base32
3117 "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
3118 (patches (search-patches "jacal-fix-texinfo.patch"))))
3119 (build-system gnu-build-system)
3120 (arguments
3121 `(#:phases
3122 (modify-phases %standard-phases
3123 (add-before 'build 'pre-build
3124 ;; Don't use upstream's script - it really doesn't fit into
3125 ;; Guix's functional paradigm.
3126 (lambda* (#:key inputs outputs #:allow-other-keys)
3127 (substitute* "Makefile"
3128 (("^install: install-script") "install: "))))
3129 (add-after 'install 'post-install
3130 ;; Instead, we provide our own simplified script.
3131 (lambda* (#:key inputs outputs #:allow-other-keys)
3132 (let ((wrapper (string-append (assoc-ref outputs "out")
3133 "/bin/jacal")))
3134 (format (open wrapper (logior O_WRONLY O_CREAT))
3135 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
3136 "-e '(slib:load \"~a/lib/jacal/math\") "
3137 "(math)' \"$@\"\n")
3138 (which "bash")
3139 (assoc-ref inputs "scm")
3140 (assoc-ref outputs "out"))
3141 (chmod wrapper #o555))))
3142 (replace 'configure
3143 (lambda* (#:key inputs outputs #:allow-other-keys)
3144 (zero? (system* "./configure"
3145 (string-append "--prefix="
3146 (assoc-ref outputs "out")))))))))
3147 (inputs `(("scm" ,scm)))
3148 (native-inputs `(("unzip" ,unzip)
3149 ("texinfo" ,texinfo)))
3150 (synopsis "Symbolic mathematics system")
3151 (description "GNU JACAL is an interactive symbolic mathematics program based on
3152Scheme. It manipulate and simplify a range of mathematical expressions such
3153as equations, scalars, vectors, and matrices.")
6fd52309 3154 (home-page "https://www.gnu.org/software/jacal/")
479c4273
JD		 3155 (license license:gpl3+)))
3156
jackhill's copy of GNU Guix: https://guix.gnu.org/