Commit | Line | Data |
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8f21aa22 | 1 | ;;; GNU Guix --- Functional package management for GNU |
1f519e8b | 2 | ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com> |
5125d005 | 3 | ;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> |
41b11c45 | 4 | ;;; Copyright © 2022 Eric Bavier <bavier@posteo.net> |
8f21aa22 PG |
5 | ;;; |
6 | ;;; This file is part of GNU Guix. | |
7 | ;;; | |
8 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
9 | ;;; under the terms of the GNU General Public License as published by | |
10 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
11 | ;;; your option) any later version. | |
12 | ;;; | |
13 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
14 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
15 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
16 | ;;; GNU General Public License for more details. | |
17 | ;;; | |
18 | ;;; You should have received a copy of the GNU General Public License | |
19 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
20 | ||
21 | (define-module (gnu packages simulation) | |
22 | #:use-module (gnu packages) | |
0ace6c0b | 23 | #:use-module (gnu packages algebra) |
40fc8992 | 24 | #:use-module (gnu packages admin) |
8f21aa22 PG |
25 | #:use-module (gnu packages base) |
26 | #:use-module (gnu packages bash) | |
27 | #:use-module (gnu packages bison) | |
28 | #:use-module (gnu packages boost) | |
f7a4757a | 29 | #:use-module (gnu packages check) |
0ace6c0b | 30 | #:use-module (gnu packages cmake) |
8f21aa22 PG |
31 | #:use-module (gnu packages compression) |
32 | #:use-module (gnu packages flex) | |
33 | #:use-module (gnu packages gettext) | |
34 | #:use-module (gnu packages gcc) | |
35 | #:use-module (gnu packages gl) | |
36 | #:use-module (gnu packages graphics) | |
37 | #:use-module (gnu packages gtk) | |
38 | #:use-module (gnu packages linux) | |
39 | #:use-module (gnu packages m4) | |
40 | #:use-module (gnu packages maths) | |
41 | #:use-module (gnu packages mpi) | |
42 | #:use-module (gnu packages multiprecision) | |
43 | #:use-module (gnu packages ncurses) | |
0ace6c0b | 44 | #:use-module (gnu packages pkg-config) |
f7a4757a | 45 | #:use-module (gnu packages python) |
3af31bc2 | 46 | #:use-module (gnu packages python-build) |
b05a1eb5 | 47 | #:use-module (gnu packages python-science) |
44d10b1f | 48 | #:use-module (gnu packages python-xyz) |
8f21aa22 PG |
49 | #:use-module (gnu packages readline) |
50 | #:use-module (gnu packages tls) | |
51 | #:use-module (gnu packages version-control) | |
52 | #:use-module (gnu packages xml) | |
53 | #:use-module (gnu packages xorg) | |
54 | #:use-module (guix download) | |
5125d005 | 55 | #:use-module (guix gexp) |
b05a1eb5 | 56 | #:use-module (guix git-download) |
40fc8992 | 57 | #:use-module (guix svn-download) |
0ace6c0b | 58 | #:use-module (guix build-system cmake) |
8f21aa22 | 59 | #:use-module (guix build-system gnu) |
f7a4757a | 60 | #:use-module (guix build-system python) |
8f21aa22 PG |
61 | #:use-module ((guix licenses) #:prefix license:) |
62 | #:use-module (guix packages) | |
63 | #:use-module (guix utils) | |
64 | #:use-module (ice-9 ftw) | |
65 | #:use-module (ice-9 regex) | |
66 | #:use-module (srfi srfi-1)) | |
67 | ||
68 | (define-public openfoam | |
69 | (package | |
70 | (name "openfoam") | |
71 | (version "4.1") | |
72 | (source | |
73 | (origin | |
74 | (method url-fetch) | |
75 | (uri (string-append | |
76 | "http://dl.openfoam.org/source/" | |
77 | (string-map (lambda (x) (if (eq? x #\.) #\- x)) version))) | |
78 | (file-name (string-append name "-" version ".tar.gz")) | |
79 | (sha256 | |
80 | (base32 "0cgxh4h2hf50qbvvdg5miwc2nympb0nrv3md96vb3gbs9vk8vq9d")) | |
886d833e LC |
81 | (patches (search-patches "openfoam-4.1-cleanup.patch")) |
82 | (modules '((guix build utils))) | |
83 | (snippet | |
84 | '(begin | |
85 | ;; Include <sys/sysmacros.h>, which is where glibc >= 2.28 provides | |
86 | ;; 'major' and 'minor'. | |
87 | (substitute* "src/OSspecific/POSIX/fileStat.C" | |
88 | (("#include <unistd\\.h>") | |
89 | "#include <unistd.h>\n#include <sys/sysmacros.h>\n")) | |
90 | #t)))) | |
8f21aa22 PG |
91 | (build-system gnu-build-system) |
92 | (inputs | |
93 | `(("boost" ,boost) | |
94 | ("cgal" ,cgal) | |
95 | ("flex" ,flex) | |
96 | ("git" ,git) | |
97 | ("gmp" ,gmp) | |
98 | ("libxt" ,libxt) | |
99 | ("metis" ,metis) | |
100 | ("mpfr" ,mpfr) | |
101 | ("ncurses" ,ncurses) | |
102 | ("readline" ,readline) | |
103 | ("scotch" ,pt-scotch32) | |
104 | ("zlib" ,zlib))) | |
105 | (native-inputs | |
8394619b | 106 | (list bison)) |
8f21aa22 | 107 | (propagated-inputs |
8394619b | 108 | (list gzip gnuplot openmpi)) |
f1de0e37 DL |
109 | (outputs '("debug" ;~60MB |
110 | "out")) | |
8f21aa22 PG |
111 | (arguments |
112 | `( ;; Executable files and shared libraries are located in the 'platforms' | |
113 | ;; subdirectory. | |
114 | #:strip-directories (list (string-append | |
115 | "lib/OpenFOAM-" ,version | |
116 | "/platforms/linux64GccDPInt32Opt/bin") | |
117 | (string-append | |
118 | "lib/OpenFOAM-" ,version | |
119 | "/platforms/linux64GccDPInt32Opt/lib")) | |
120 | #:tests? #f ; no tests to run | |
121 | ||
122 | #:modules ((ice-9 ftw) | |
123 | (ice-9 regex) | |
124 | (guix build gnu-build-system) | |
125 | (guix build utils)) | |
126 | ||
127 | #:phases (modify-phases %standard-phases | |
128 | (add-after 'unpack 'rename-build-directory | |
129 | (lambda _ | |
130 | (chdir "..") | |
131 | ;; Use 'OpenFOAM-version' convention to match the file | |
132 | ;; name expectations in the build phase. | |
133 | (let ((unpack-dir (string-append | |
134 | (getcwd) "/" | |
135 | (list-ref (scandir (getcwd) (lambda (name) | |
136 | (string-match "^OpenFOAM" name))) 0))) | |
137 | (build-dir (string-append | |
138 | (getcwd) "/OpenFOAM-" ,version))) | |
139 | (rename-file unpack-dir build-dir) ; rename build directory | |
140 | (chdir (basename build-dir))) ; move to build directory | |
141 | #t)) | |
142 | (delete 'configure) ; no configure phase | |
143 | (replace 'build | |
144 | (lambda _ | |
145 | (let ((libraries '("boost" "cgal" "gmp" "metis" "mpfr" "scotch"))) | |
146 | ;; set variables to define store paths | |
147 | (for-each (lambda (library) | |
148 | (setenv (string-append | |
149 | (string-upcase library) "_ROOT") | |
150 | (assoc-ref %build-inputs library))) libraries)) | |
151 | ;; set variables to define package versions | |
152 | (setenv "SCOTCHVERSION" ,(package-version scotch)) | |
153 | (setenv "METISVERSION" ,(package-version metis)) | |
154 | ;; set variable to pass extra 'rpath' arguments to linker | |
155 | (setenv "LDFLAGS" | |
156 | (string-append | |
157 | "-Wl," | |
158 | "-rpath=" %output "/lib/OpenFOAM-" ,version | |
159 | "/platforms/linux64GccDPInt32Opt/lib," | |
160 | "-rpath=" %output "/lib/OpenFOAM-" ,version | |
161 | "/platforms/linux64GccDPInt32Opt/lib/dummy")) | |
162 | ;; compile OpenFOAM libraries and applications | |
163 | (zero? (system (format #f | |
164 | "source ./etc/bashrc && ./Allwmake -j~a" | |
165 | (parallel-job-count)))))) | |
166 | (add-after 'build 'update-configuration-files | |
167 | (lambda _ | |
168 | ;; record store paths and package versions in | |
169 | ;; configuration files | |
170 | (substitute* "etc/config.sh/CGAL" | |
171 | (("$BOOST_ROOT") (getenv "BOOST_ROOT"))) | |
172 | (substitute* "etc/config.sh/CGAL" | |
173 | (("$CGAL_ROOT") (getenv "CGAL_ROOT"))) | |
174 | (substitute* "etc/config.sh/metis" | |
175 | (("$METIS_ROOT") (getenv "METIS_ROOT"))) | |
176 | (substitute* "etc/config.sh/metis" | |
177 | (("$METISVERSION") (getenv "METISVERSION"))) | |
178 | (substitute* "etc/config.sh/scotch" | |
179 | (("$SCOTCH_ROOT") (getenv "SCOTCH_ROOT"))) | |
180 | (substitute* "etc/config.sh/scotch" | |
181 | (("$SCOTCHVERSION") (getenv "SCOTCHVERSION"))) | |
182 | (substitute* "etc/config.sh/settings" | |
183 | (("$GMP_ROOT") (getenv "GMP_ROOT"))) | |
184 | (substitute* "etc/config.sh/settings" | |
185 | (("$MPFR_ROOT") (getenv "MPFR_ROOT"))) | |
186 | ;; reset lockDir variable to refer to write-enabled | |
187 | ;; directory | |
188 | (substitute* "wmake/wmake" | |
189 | ((" lockDir=.*$") | |
190 | " lockDir=$HOME/.$WM_PROJECT/.wmake\n")) | |
191 | (substitute* "wmake/wmakeScheduler" | |
192 | (("lockDir=.*$") | |
193 | "lockDir=$HOME/.$WM_PROJECT/.wmake\n")) | |
194 | (substitute* "wmake/wmakeSchedulerUptime" | |
195 | (("lockDir=.*$") | |
196 | "lockDir=$HOME/.$WM_PROJECT/.wmake\n")) | |
197 | #t)) | |
f1de0e37 DL |
198 | (add-after 'build 'cleanup |
199 | ;; Avoid unncessary, voluminous object and dep files. | |
200 | (lambda _ | |
201 | (delete-file-recursively | |
202 | "platforms/linux64GccDPInt32Opt/src") | |
203 | (delete-file-recursively | |
204 | "platforms/linux64GccDPInt32OptSYSTEMOPENMPI") | |
205 | (for-each delete-file (find-files "." "\\.o$")) | |
206 | #t)) | |
8f21aa22 PG |
207 | (replace 'install |
208 | (lambda _ | |
209 | ;; use 'OpenFOAM-version' convention | |
210 | (let ((install-dir (string-append | |
211 | %output "/lib/OpenFOAM-" ,version))) | |
212 | (mkdir-p install-dir) ; create install directory | |
213 | ;; move contents of build directory to install directory | |
214 | (copy-recursively "." install-dir)))) | |
215 | (add-after 'install 'add-symbolic-link | |
216 | (lambda _ | |
217 | ;; add symbolic link for standard 'bin' directory | |
218 | (symlink | |
219 | (string-append "./lib/OpenFOAM-" ,version | |
220 | "/platforms/linux64GccDPInt32Opt/bin") | |
221 | (string-append %output "/bin")) | |
222 | #t))))) | |
223 | ;; Note: | |
224 | ;; Tutorial files are installed read-only in /gnu/store. | |
225 | ;; To allow write permissions on files copied from the store a | |
226 | ;; 'chmod' step is needed before running the applications. For | |
227 | ;; example, from a user's login: | |
228 | ;; $ source $GUIX_PROFILE/lib/OpenFOAM-4.1/etc/bashrc | |
229 | ;; $ mkdir -p $FOAM_RUN | |
230 | ;; $ cd $FOAM_RUN | |
a836e9f5 PG |
231 | ;; $ cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/pitzDaily . |
232 | ;; $ cd pitzDaily | |
8f21aa22 PG |
233 | ;; $ chmod -R u+w . |
234 | ;; $ blockMesh | |
235 | (synopsis "Framework for numerical simulation of fluid flow") | |
236 | (description "OpenFOAM provides a set of solvers and methods for tackling | |
237 | problems in the field of Computational Fluid Dynamics (CFD). It is written in | |
238 | C++. Governing equations such as the Navier-Stokes equations can be solved in | |
239 | integral form. Physical processes such as phase change, droplet transport and | |
240 | chemical reaction can be modelled. Numerical methods are included to deal with | |
241 | sharp gradients, such as those encountered in flows with shock waves and flows | |
242 | with gas/liquid interfaces. Large problems may be split into smaller, connected | |
b6598237 | 243 | problems for efficient solution on parallel systems.") |
8f21aa22 PG |
244 | (license license:gpl3+) |
245 | (home-page "https://openfoam.org"))) | |
f7a4757a PG |
246 | |
247 | (define-public python-fenics-dijitso | |
248 | (package | |
249 | (name "python-fenics-dijitso") | |
23686184 | 250 | (version "2019.1.0") |
f7a4757a PG |
251 | (source |
252 | (origin | |
253 | (method url-fetch) | |
254 | (uri (pypi-uri "fenics-dijitso" version)) | |
255 | (sha256 | |
256 | (base32 | |
23686184 | 257 | "0lhqsq8ypdak0ahr2jnyvg07yrqp6wicjxi6k56zx24wp3qg60sc")))) |
f7a4757a PG |
258 | (build-system python-build-system) |
259 | (inputs | |
8394619b | 260 | (list openmpi python-numpy)) |
f7a4757a | 261 | (native-inputs |
8394619b | 262 | (list python-pytest-cov)) |
f7a4757a | 263 | (propagated-inputs |
8394619b | 264 | (list python-mpi4py)) |
f7a4757a PG |
265 | (arguments |
266 | `(#:phases | |
267 | (modify-phases %standard-phases | |
268 | (add-after 'build 'mpi-setup | |
269 | ,%openmpi-setup) | |
270 | (replace 'check | |
271 | (lambda _ | |
272 | (setenv "HOME" "/tmp") | |
f7a4757a | 273 | (with-directory-excursion "test" |
7a82074c PG |
274 | ;; Disable parallel tests to avoid race condition. See |
275 | ;; https://github.com/pytest-dev/pytest-cov/issues/237. | |
276 | (substitute* "runtests.sh" | |
277 | (("for p in 1 4 8 16; do") | |
278 | "for p in 1; do")) | |
85b42f04 | 279 | (invoke "./runtests.sh"))))))) |
f7a4757a PG |
280 | (home-page "https://bitbucket.org/fenics-project/dijitso/") |
281 | (synopsis "Distributed just-in-time building of shared libraries") | |
282 | (description | |
283 | "Dijitso provides a core component of the @code{FEniCS} framework, | |
284 | namely the just-in-time compilation of C++ code that is generated from | |
285 | Python modules. It is called from within a C++ library, using ctypes | |
286 | to import the dynamic shared library directly. | |
287 | ||
288 | As long as the compiled code can provide a simple factory function to | |
289 | a class implementing a predefined C++ interface, there is no limit to | |
290 | the complexity of that interface. Parallel support depends on the | |
291 | @code{mpi4py} interface.") | |
292 | (license license:lgpl3+))) | |
3941cf5a PG |
293 | |
294 | (define-public python-fenics-ufl | |
295 | (package | |
296 | (name "python-fenics-ufl") | |
def588d2 | 297 | (version "2019.1.0") |
3941cf5a PG |
298 | (source |
299 | (origin | |
300 | (method url-fetch) | |
301 | (uri (pypi-uri "fenics-ufl" version)) | |
302 | (sha256 | |
303 | (base32 | |
def588d2 | 304 | "10dz8x3lm68x2w3kkqcjask38h0zkhhak26jdbkppr8g9y8wny7p")))) |
3941cf5a PG |
305 | (build-system python-build-system) |
306 | (inputs | |
8394619b | 307 | (list python-numpy)) |
3941cf5a | 308 | (native-inputs |
8394619b | 309 | (list python-pytest)) |
3941cf5a PG |
310 | (arguments |
311 | '(#:phases | |
312 | (modify-phases %standard-phases | |
313 | (replace 'check | |
314 | (lambda _ | |
10bee15c | 315 | (invoke "py.test" "test")))))) |
3941cf5a PG |
316 | (home-page "https://bitbucket.org/fenics-project/ufl/") |
317 | (synopsis "Unified language for form-compilers") | |
318 | (description "The Unified Form Language (UFL) is a domain specific | |
319 | language for declaration of finite element discretizations of | |
320 | variational forms. More precisely, it defines a flexible interface | |
321 | for choosing finite element spaces and defining expressions for weak | |
322 | forms in a notation close to mathematical notation. | |
323 | ||
324 | UFL is part of the FEniCS Project.") | |
325 | (license license:lgpl3+))) | |
0fc49983 PG |
326 | |
327 | (define-public python-fenics-fiat | |
328 | (package | |
329 | (name "python-fenics-fiat") | |
4dfb22c1 | 330 | (version "2019.1.0") |
0fc49983 PG |
331 | (source |
332 | (origin | |
333 | (method url-fetch) | |
334 | (uri (pypi-uri "fenics-fiat" version)) | |
335 | (sha256 | |
336 | (base32 | |
4dfb22c1 | 337 | "13sc7lma3d2mh43an7i4kkdbbk4cmvxjk45wi43xnjd7qc38zg4b")))) |
0fc49983 PG |
338 | (build-system python-build-system) |
339 | (native-inputs | |
8394619b | 340 | (list python-pytest)) |
0fc49983 | 341 | (propagated-inputs |
8394619b | 342 | (list python-numpy python-sympy)) |
0fc49983 PG |
343 | (arguments |
344 | '(#:phases | |
345 | (modify-phases %standard-phases | |
346 | (replace 'check | |
347 | (lambda _ | |
0fc49983 | 348 | (with-directory-excursion "test" |
4dfb22c1 PG |
349 | ;; FIXME: three FIAT test modules are known to fail |
350 | ;; with recent versions of pytest (>= 4). These are | |
351 | ;; skipped for FIAT version 2019.1.0 pending an | |
352 | ;; upstream pull request. For details see request #59 | |
353 | ;; at https://bitbucket.org/fenics-project/fiat/. | |
354 | (invoke "py.test" "unit/" | |
355 | "--ignore=unit/test_fiat.py" | |
356 | "--ignore=unit/test_quadrature.py" | |
0c9844e1 | 357 | "--ignore=unit/test_reference_element.py"))))))) |
0fc49983 PG |
358 | (home-page "https://bitbucket.org/fenics-project/fiat/") |
359 | (synopsis "Tabulation of finite element function spaces") | |
360 | (description | |
361 | "The FInite element Automatic Tabulator (FIAT) supports | |
362 | generation of arbitrary order instances of the Lagrange elements on | |
363 | lines, triangles, and tetrahedra. It is also capable of generating | |
364 | arbitrary order instances of Jacobi-type quadrature rules on the same | |
365 | element shapes. Further, H(div) and H(curl) conforming finite element | |
366 | spaces such as the families of Raviart-Thomas, Brezzi-Douglas-Marini | |
367 | and Nedelec are supported on triangles and tetrahedra. Upcoming | |
368 | versions will also support Hermite and nonconforming elements. | |
369 | ||
370 | FIAT is part of the FEniCS Project.") | |
371 | (license license:lgpl3+))) | |
6b7f1f8a PG |
372 | |
373 | (define-public python-fenics-ffc | |
374 | (package | |
375 | (name "python-fenics-ffc") | |
ec8dff89 | 376 | (version "2019.1.0.post0") |
6b7f1f8a PG |
377 | (source |
378 | (origin | |
379 | (method url-fetch) | |
380 | (uri (pypi-uri "fenics-ffc" version)) | |
381 | (sha256 | |
382 | (base32 | |
ec8dff89 | 383 | "1f2a44ha65fg3a1prrbrsz4dgvibsv0j5c3pi2m52zi93bhwwgg9")))) |
6b7f1f8a PG |
384 | (build-system python-build-system) |
385 | (native-inputs | |
8394619b | 386 | (list python-pytest)) |
6b7f1f8a | 387 | (propagated-inputs |
8394619b | 388 | (list python-fenics-dijitso python-fenics-fiat python-fenics-ufl)) |
6b7f1f8a PG |
389 | (arguments |
390 | '(#:phases | |
391 | (modify-phases %standard-phases | |
392 | (replace 'check | |
393 | (lambda _ | |
394 | (setenv "HOME" (getcwd)) | |
6b7f1f8a PG |
395 | (with-directory-excursion "test" |
396 | ;; FIXME: the tests in subdirectory | |
397 | ;; 'unit/ufc/finite_element' require the ffc_factory | |
398 | ;; extension module. This module, located in the 'libs' | |
399 | ;; subdirectory, needs to be built and made accessible | |
400 | ;; prior to running the tests. | |
401 | (invoke "py.test" "unit/" "--ignore=unit/ufc/") | |
402 | (with-directory-excursion "uflacs" | |
1ebb629c MC |
403 | (invoke "py.test" "unit/"))) |
404 | #t))))) | |
6b7f1f8a PG |
405 | (home-page "https://bitbucket.org/fenics-project/ffc/") |
406 | (synopsis "Compiler for finite element variational forms") | |
407 | (description "The FEniCS Form Compiler (FFC) is a compiler for | |
408 | finite element variational forms. From a high-level description of | |
409 | the form, it generates efficient low-level C++ code that can be used | |
410 | to assemble the corresponding discrete operator (tensor). In | |
411 | particular, a bilinear form may be assembled into a matrix and a | |
412 | linear form may be assembled into a vector. FFC may be used either | |
413 | from the command line (by invoking the @code{ffc} command) or as a | |
414 | Python module (@code{import ffc}). | |
415 | ||
416 | FFC is part of the FEniCS Project.") | |
417 | ;; There are two files released with a public domain licence; | |
418 | ;; ufc.h and ufc_geometry.h, in subdirectory 'ffc/backends/ufc'. | |
419 | (license (list license:public-domain license:lgpl3+)))) | |
0ace6c0b PG |
420 | |
421 | (define-public fenics-dolfin | |
422 | (package | |
423 | (name "fenics-dolfin") | |
09ecd9a7 | 424 | (version "2019.1.0.post0") |
0ace6c0b PG |
425 | (source |
426 | (origin | |
427 | (method url-fetch) | |
428 | (uri (string-append | |
429 | "https://bitbucket.org/fenics-project/dolfin/get/" | |
430 | version ".tar.gz")) | |
431 | (file-name (string-append name "-" version ".tar.gz")) | |
432 | (sha256 | |
433 | (base32 | |
09ecd9a7 | 434 | "1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0")) |
41b11c45 EB |
435 | (patches (search-patches "fenics-dolfin-algorithm.patch" |
436 | "fenics-dolfin-demo-init.patch" | |
437 | "fenics-dolfin-boost.patch" | |
438 | "fenics-dolfin-config-slepc.patch")) | |
0ace6c0b PG |
439 | (modules '((guix build utils))) |
440 | (snippet | |
441 | '(begin | |
442 | ;; Make sure we don't use the bundled test framework. | |
443 | (delete-file-recursively "test/unit/cpp/catch") | |
444 | (substitute* "test/unit/cpp/main.cpp" | |
445 | ;; Use standard search paths for 'catch' header file. | |
446 | (("#include.*") | |
447 | "#include <catch.hpp>\n")) | |
448 | (substitute* "test/unit/cpp/CMakeLists.txt" | |
09ecd9a7 | 449 | ;; Specify directory to find the header file. |
0ace6c0b PG |
450 | (("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back) |
451 | (string-append front | |
69505bec | 452 | "$ENV{CATCH_DIR}/include" back "\n"))))))) |
0ace6c0b PG |
453 | (build-system cmake-build-system) |
454 | (inputs | |
455 | `(("blas" ,openblas) | |
456 | ("boost" ,boost) | |
457 | ("eigen" ,eigen) | |
458 | ("hdf5" ,hdf5-parallel-openmpi) | |
459 | ("lapack" ,lapack) | |
460 | ("libxml2" ,libxml2) | |
461 | ("openmpi" ,openmpi) | |
462 | ("python" ,python-3) | |
463 | ("scotch" ,pt-scotch32) | |
464 | ("suitesparse" ,suitesparse) | |
465 | ("sundials" ,sundials-openmpi) | |
466 | ("zlib" ,zlib))) | |
467 | (native-inputs | |
b736af18 | 468 | `(("catch" ,catch2-1) |
0ace6c0b PG |
469 | ("pkg-config" ,pkg-config))) |
470 | (propagated-inputs | |
471 | `(("ffc" ,python-fenics-ffc) | |
472 | ("petsc" ,petsc-openmpi) | |
473 | ("slepc" ,slepc-openmpi))) | |
474 | (arguments | |
475 | `(#:configure-flags | |
476 | `("-DDOLFIN_ENABLE_DOCS:BOOL=OFF" | |
477 | "-DDOLFIN_ENABLE_HDF5:BOOL=ON" | |
478 | "-DDOLFIN_ENABLE_MPI:BOOL=ON" | |
479 | "-DDOLFIN_ENABLE_PARMETIS:BOOL=OFF" | |
480 | "-DDOLFIN_ENABLE_SCOTCH:BOOL=ON" | |
481 | "-DDOLFIN_ENABLE_SUNDIALS:BOOL=ON" | |
482 | "-DDOLFIN_ENABLE_TRILINOS:BOOL=OFF") | |
483 | #:phases | |
484 | (modify-phases %standard-phases | |
485 | (add-after 'patch-usr-bin-file 'mpi-setup | |
486 | ,%openmpi-setup) | |
487 | (add-after 'patch-source-shebangs 'set-paths | |
488 | (lambda _ | |
489 | ;; Define paths to store locations. | |
490 | (setenv "BLAS_DIR" (assoc-ref %build-inputs "blas")) | |
491 | (setenv "CATCH_DIR" (assoc-ref %build-inputs "catch")) | |
492 | (setenv "LAPACK_DIR" (assoc-ref %build-inputs "lapack")) | |
493 | (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) | |
494 | (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) | |
495 | (setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch")) | |
496 | (setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials")) | |
69505bec | 497 | (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse")))) |
0ace6c0b PG |
498 | (add-before 'check 'pre-check |
499 | (lambda _ | |
500 | ;; The Dolfin repository uses git-lfs, whereby web links are | |
501 | ;; substituted for large files. Guix does not currently support | |
502 | ;; git-lfs, so only the links are downloaded. The tests that | |
503 | ;; require the absent meshes cannot run and are skipped. | |
504 | ;; | |
41b11c45 EB |
505 | ;; One serial test fails and is skipped. |
506 | ;; i) demo_multimesh-stokes_serial: | |
0ace6c0b PG |
507 | ;; Warning: Found no facets matching domain for boundary |
508 | ;; condition. | |
509 | ;; | |
510 | ;; One mpi test fails and is skipped. | |
511 | ;; i) demo_stokes-iterative_mpi: | |
512 | ;; The MPI_Comm_rank() function was called before MPI_INIT was | |
513 | ;; invoked | |
514 | (call-with-output-file "CTestCustom.cmake" | |
515 | (lambda (port) | |
516 | (display | |
517 | (string-append | |
518 | "set(CTEST_CUSTOM_TESTS_IGNORE " | |
519 | "demo_bcs_serial " | |
520 | "demo_bcs_mpi " | |
521 | "demo_eigenvalue_serial " | |
522 | "demo_eigenvalue_mpi " | |
523 | "demo_navier-stokes_serial " | |
524 | "demo_navier-stokes_mpi " | |
525 | "demo_stokes-taylor-hood_serial " | |
526 | "demo_stokes-taylor-hood_mpi " | |
527 | "demo_subdomains_serial " | |
528 | "demo_advection-diffusion_serial " | |
529 | "demo_advection-diffusion_mpi " | |
530 | "demo_auto-adaptive-navier-stokes_serial " | |
531 | "demo_contact-vi-snes_serial " | |
532 | "demo_contact-vi-snes_mpi " | |
533 | "demo_contact-vi-tao_serial " | |
534 | "demo_contact-vi-tao_mpi " | |
535 | "demo_curl-curl_serial " | |
536 | "demo_curl-curl_mpi " | |
537 | "demo_dg-advection-diffusion_serial " | |
538 | "demo_dg-advection-diffusion_mpi " | |
539 | "demo_elasticity_serial " | |
540 | "demo_elasticity_mpi " | |
541 | "demo_elastodynamics_serial " | |
542 | "demo_elastodynamics_mpi " | |
543 | "demo_lift-drag_serial " | |
544 | "demo_lift-drag_mpi " | |
545 | "demo_mesh-quality_serial " | |
546 | "demo_mesh-quality_mpi " | |
547 | "demo_multimesh-stokes_serial " | |
69505bec | 548 | ")\n") port))))) |
0ace6c0b | 549 | (replace 'check |
69505bec PP |
550 | (lambda* (#:key tests? #:allow-other-keys) |
551 | (when tests? | |
552 | (invoke "make" "unittests") | |
553 | (invoke "make" "demos") | |
554 | (invoke "ctest" "-R" "unittests") | |
555 | (invoke "ctest" "-R" "demo" "-R" "serial") | |
556 | (invoke "ctest" "-R" "demo" "-R" "mpi"))))))) | |
0ace6c0b PG |
557 | (home-page "https://bitbucket.org/fenics-project/dolfin/") |
558 | (synopsis "Problem solving environment for differential equations") | |
559 | (description | |
560 | "DOLFIN is a computational framework for finding numerical | |
561 | solutions to problems described by differential equations. Numerical | |
562 | models in DOLFIN are constructed using general families of finite | |
563 | elements. Data structures are provided for discretizing the governing | |
564 | system on a computational mesh. A compact syntax, similar to | |
565 | mathematical notation, is made available for defining function spaces | |
566 | and expressing variational forms. Interfaces to specialized matrix | |
567 | solvers are provided for solving the resultant linear systems. | |
568 | ||
569 | @code{fenics-dolfin} is part of the FEniCS project. It is the C++ | |
570 | user interface to the FEniCS core components and external libraries.") | |
571 | ;; The source code for the DOLFIN C++ library is licensed under the | |
572 | ;; GNU Lesser General Public License, version 3 or later, with the | |
573 | ;; following exceptions: | |
574 | ;; | |
575 | ;; public-domain: dolfin/geometry/predicates.cpp | |
576 | ;; dolfin/geometry/predicates.h | |
577 | ;; | |
578 | ;; zlib: dolfin/io/base64.cpp | |
579 | ;; dolfin/io/base64.h | |
580 | ;; | |
581 | ;; expat: dolfin/io/pugiconfig.hpp | |
582 | ;; dolfin/io/pugixml.cpp | |
583 | ;; dolfin/io/pugixml.hpp | |
584 | (license (list license:public-domain | |
585 | license:zlib | |
586 | license:expat | |
587 | license:lgpl3+)))) | |
ae0f1dd1 PG |
588 | |
589 | (define-public fenics | |
1a265842 | 590 | (package/inherit fenics-dolfin |
ae0f1dd1 PG |
591 | (name "fenics") |
592 | (build-system python-build-system) | |
593 | (inputs | |
594 | `(("pybind11" ,pybind11) | |
595 | ("python-matplotlib" ,python-matplotlib) | |
596 | ,@(alist-delete "python" (package-inputs fenics-dolfin)))) | |
597 | (native-inputs | |
c69959f0 | 598 | `(("cmake" ,cmake-minimal) |
ae0f1dd1 PG |
599 | ("ply" ,python-ply) |
600 | ("pytest" ,python-pytest) | |
601 | ("python-decorator" ,python-decorator) | |
602 | ("python-pkgconfig" ,python-pkgconfig) | |
603 | ,@(package-native-inputs fenics-dolfin))) | |
604 | (propagated-inputs | |
605 | `(("dolfin" ,fenics-dolfin) | |
606 | ("petsc4py" ,python-petsc4py) | |
607 | ("slepc4py" ,python-slepc4py))) | |
608 | (arguments | |
609 | `(#:phases | |
610 | (modify-phases %standard-phases | |
b7d2644c PP |
611 | (add-after 'unpack 'relax-requirements |
612 | (lambda _ | |
613 | (substitute* "python/setup.py" | |
614 | (("pybind11==") "pybind11>=")))) | |
ae0f1dd1 PG |
615 | (add-after 'patch-source-shebangs 'set-paths |
616 | (lambda _ | |
617 | ;; Define paths to store locations. | |
618 | (setenv "PYBIND11_DIR" (assoc-ref %build-inputs "pybind11")) | |
619 | ;; Move to python sub-directory. | |
1ebb629c | 620 | (chdir "python"))) |
ae0f1dd1 PG |
621 | (add-after 'build 'mpi-setup |
622 | ,%openmpi-setup) | |
623 | (add-before 'check 'pre-check | |
624 | (lambda _ | |
37bb0d1e PG |
625 | ;; Exclude three tests that generate |
626 | ;; 'NotImplementedError' in matplotlib version 3.1.2. | |
627 | ;; See | |
628 | ;; <https://github.com/matplotlib/matplotlib/issues/15382>. | |
629 | ;; Also exclude tests that require meshes supplied by | |
630 | ;; git-lfs. | |
ae0f1dd1 PG |
631 | (substitute* "demo/test.py" |
632 | (("(.*stem !.*)" line) | |
633 | (string-append | |
634 | line "\n" | |
635 | "excludeList = [\n" | |
37bb0d1e PG |
636 | "'built-in-meshes', \n" |
637 | "'hyperelasticity', \n" | |
638 | "'elasticity', \n" | |
ae0f1dd1 PG |
639 | "'multimesh-quadrature', \n" |
640 | "'multimesh-marking', \n" | |
641 | "'mixed-poisson-sphere', \n" | |
642 | "'mesh-quality', \n" | |
643 | "'lift-drag', \n" | |
644 | "'elastodynamics', \n" | |
645 | "'dg-advection-diffusion', \n" | |
dd6cb4a0 | 646 | "'curl-curl', \n" |
ae0f1dd1 PG |
647 | "'contact-vi-tao', \n" |
648 | "'contact-vi-snes', \n" | |
649 | "'collision-detection', \n" | |
650 | "'buckling-tao', \n" | |
651 | "'auto-adaptive-navier-stokes', \n" | |
652 | "'advection-diffusion', \n" | |
653 | "'subdomains', \n" | |
654 | "'stokes-taylor-hood', \n" | |
655 | "'stokes-mini', \n" | |
656 | "'navier-stokes', \n" | |
657 | "'eigenvalue']\n" | |
658 | "demos = [" | |
659 | "d for d in demos if d[0].stem not in " | |
660 | "excludeList]\n"))) | |
661 | (setenv "HOME" (getcwd)) | |
ae0f1dd1 | 662 | ;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP. |
1ebb629c | 663 | (setenv "OPENBLAS_NUM_THREADS" "1"))) |
ae0f1dd1 | 664 | (replace 'check |
9d5160bc PP |
665 | (lambda* (#:key tests? #:allow-other-keys) |
666 | (when tests? | |
667 | (with-directory-excursion "test" | |
b13966a9 OL |
668 | (invoke |
669 | "pytest" "unit" | |
670 | ;; The test test_snes_set_from_options() in the file | |
671 | ;; unit/nls/test_PETScSNES_solver.py fails and is ignored. | |
672 | "--ignore" "unit/nls/test_PETScSNES_solver.py" | |
673 | ;; Fails with a segfault. | |
674 | "--ignore" "unit/io/test_XDMF.py"))))) | |
ae0f1dd1 PG |
675 | (add-after 'install 'install-demo-files |
676 | (lambda* (#:key outputs #:allow-other-keys) | |
677 | (let* ((demos (string-append | |
678 | (assoc-ref outputs "out") | |
679 | "/share/python-dolfin/demo"))) | |
680 | (mkdir-p demos) | |
681 | (with-directory-excursion "demo" | |
682 | (for-each (lambda (file) | |
683 | (let* ((dir (dirname file)) | |
684 | (tgt-dir (string-append demos "/" dir))) | |
685 | (unless (equal? "." dir) | |
686 | (mkdir-p tgt-dir) | |
687 | (install-file file tgt-dir)))) | |
1ebb629c | 688 | (find-files "." ".*\\.(py|gz|xdmf)$"))))))))) |
ae0f1dd1 PG |
689 | (home-page "https://fenicsproject.org/") |
690 | (synopsis "High-level environment for solving differential equations") | |
691 | (description | |
692 | "@code{fenics} is a computing platform for solving general classes of | |
693 | problems that involve differential equations. @code{fenics} facilitates | |
694 | access to efficient methods for dealing with ordinary differential | |
695 | equations (ODEs) and partial differential equations (PDEs). Systems of | |
696 | equations such as these are commonly encountered in areas of engineering, | |
697 | mathematics and the physical sciences. It is particularly well-suited to | |
698 | problems that can be solved using the Finite Element Method (FEM). | |
699 | ||
700 | @code{fenics} is the top level of the set of packages that are developed | |
701 | within the FEniCS project. It provides the python user interface to the | |
702 | FEniCS core components and external libraries.") | |
703 | (license license:lgpl3+))) | |
40fc8992 PG |
704 | |
705 | (define-public fullswof-2d | |
706 | (let ((revision 505) | |
707 | (release "1.09.01")) | |
708 | (package | |
709 | (name "fullswof-2d") | |
710 | (version release) | |
711 | (source (origin | |
712 | (method svn-fetch) | |
713 | (uri (svn-reference | |
714 | (url (string-append "https://subversion.renater.fr/" | |
715 | "anonscm/svn/fullswof-2d/tags/" | |
716 | "release-" version)) | |
717 | (revision revision))) | |
718 | (file-name (string-append "fullswof-2d-" version "-checkout")) | |
719 | (sha256 | |
720 | (base32 | |
721 | "16v08dx7h7n4wyddzbwimazwyj74ynis12mpjfkay4243npy44b8")))) | |
722 | (build-system gnu-build-system) | |
723 | (native-inputs | |
8394619b | 724 | (list inetutils)) ; for 'hostname', used in the check phase |
40fc8992 PG |
725 | (arguments |
726 | `(#:phases | |
727 | (modify-phases %standard-phases | |
728 | (delete 'configure) ; no configure script | |
729 | (add-after 'build 'build-tools | |
730 | (lambda _ | |
731 | (with-directory-excursion "Tools/ConvertFormat" | |
732 | (invoke "make" "../../bin/asc2xyz") | |
733 | (invoke "make" "../../bin/xyz2asc")) | |
734 | (with-directory-excursion "Tools/ExtractWindow" | |
735 | (invoke "make" "../../bin/cropxyz")) | |
736 | #t)) | |
737 | (replace 'check ; no check target | |
738 | (lambda _ | |
739 | (invoke "make" "benchref"))) | |
740 | (replace 'install ; no install target | |
741 | (lambda* (#:key outputs #:allow-other-keys) | |
742 | (let* ((out (assoc-ref outputs "out")) | |
743 | (bin (string-append out "/bin")) | |
744 | (doc (string-append | |
745 | out "/share/doc/" ,name "-" ,version)) | |
746 | (examples (string-append doc "/Examples"))) | |
747 | (with-directory-excursion "bin" | |
748 | (for-each (lambda (binary) (install-file binary bin)) | |
749 | (list "asc2xyz" "xyz2asc" "cropxyz" | |
750 | "FullSWOF_2D"))) | |
751 | (with-directory-excursion "doc" | |
752 | (for-each (lambda (pdf) (install-file pdf doc)) | |
753 | (list "Documentation.pdf" "refman.pdf"))) | |
754 | (with-directory-excursion "Tools" | |
755 | (for-each (lambda (dir) | |
756 | (copy-file | |
757 | (string-append dir "/README.txt") | |
758 | (string-append doc "/README_" dir ".txt"))) | |
759 | (list "ConvertFormat" "ExtractWindow"))) | |
760 | (copy-recursively "Examples" examples) | |
761 | #t)))))) | |
762 | (home-page "https://www.idpoisson.fr/fullswof/") | |
763 | (synopsis "Two dimensional flow solver for flood modelling") | |
764 | (description "@code{FullSWOF_2d} is a numerical tool for solving | |
765 | the shallow water equations on structured grids. The name FullSWOF | |
766 | refers to the Full form of the Shallow Water equations for Overland | |
767 | Flow. The discretized system of equations is solved using the finite | |
768 | volume method. A choice of shock-capturing methods is available to | |
769 | locate the transition boundaries between the wet areas and the dry | |
770 | areas in the model. A semi-implicit method is used to advance the | |
771 | solution in time. The tool is typically applied to the modelling of | |
772 | river flooding.") | |
773 | (license license:cecill)))) | |
1f519e8b PG |
774 | |
775 | (define-public python-meshio | |
776 | (package | |
777 | (name "python-meshio") | |
6803a29d | 778 | (version "5.3.4") |
1f519e8b | 779 | (source |
6803a29d PP |
780 | (origin |
781 | (method url-fetch) | |
782 | (uri (pypi-uri "meshio" version)) | |
783 | (sha256 | |
784 | (base32 | |
785 | "1w39qcg0rw5kb04j7sa45fnqd6k20fsdgrf62cmw2ygjgwnnjh72")) | |
786 | (snippet | |
787 | '(let ((file (open-file "setup.py" "a"))) | |
788 | (display "from setuptools import setup\nsetup()" file) | |
789 | (close-port file))))) | |
1f519e8b PG |
790 | (build-system python-build-system) |
791 | (inputs | |
4a6acd04 PP |
792 | (list python-h5py |
793 | python-netcdf4)) | |
1f519e8b | 794 | (native-inputs |
4a6acd04 | 795 | (list python-pytest)) |
1f519e8b | 796 | (propagated-inputs |
4a6acd04 | 797 | (list python-importlib-metadata |
6803a29d PP |
798 | python-numpy |
799 | python-rich)) | |
1f519e8b | 800 | (arguments |
ec27aafc | 801 | '(#:phases |
1f519e8b PG |
802 | (modify-phases %standard-phases |
803 | (replace 'check | |
ec27aafc PP |
804 | (lambda* (#:key tests? #:allow-other-keys) |
805 | (when tests? | |
806 | (invoke "python" "-m" "pytest" "-v" "tests"))))))) | |
1f519e8b PG |
807 | (home-page "https://github.com/nschloe/meshio") |
808 | (synopsis "I/O for mesh files") | |
809 | (description "There are various file formats available for | |
810 | representing unstructured meshes and mesh data. The @code{meshio} | |
811 | package is able to read and write mesh files in many formats and to | |
812 | convert files from one format to another. Formats such as cgns, h5m, | |
813 | gmsh, xdmf and vtk are supported. The package provides command-line | |
814 | tools and a collection of Python modules for programmatic use.") | |
815 | (license license:expat))) | |
3af31bc2 PG |
816 | |
817 | (define-public python-pygmsh | |
818 | (package | |
819 | (name "python-pygmsh") | |
5125d005 | 820 | (version "7.1.17") |
3af31bc2 | 821 | (source |
5125d005 MC |
822 | (origin |
823 | (method git-fetch) | |
824 | (uri (git-reference | |
825 | (url "https://github.com/nschloe/pygmsh") | |
826 | (commit (string-append "v" version)))) | |
827 | (file-name (git-file-name name version)) | |
828 | (sha256 | |
829 | (base32 | |
830 | "11flp2c4ynk1fhanf4mqyzrpd0gjbnv6afrwwc7xi3mb6ms69lr0")))) | |
3af31bc2 | 831 | (build-system python-build-system) |
3af31bc2 | 832 | (arguments |
5125d005 MC |
833 | (list |
834 | #:phases | |
835 | #~(modify-phases %standard-phases | |
836 | (add-after 'unpack 'workaround-gmsh-detection-failure | |
837 | (lambda _ | |
838 | ;; Due to lack of metadata, the gmsh Python package is not | |
839 | ;; detected although importable. | |
840 | (substitute* "pyproject.toml" | |
841 | (("\"gmsh\",") "")))) | |
842 | ;; XXX: PEP 517 manual build copied from python-isort. | |
843 | (replace 'build | |
844 | (lambda _ | |
845 | (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) | |
846 | (replace 'check | |
847 | (lambda* (#:key tests? #:allow-other-keys) | |
848 | (when tests? | |
849 | (invoke "pytest" "-v" "tests")))) | |
850 | (replace 'install | |
851 | (lambda _ | |
852 | (let ((whl (car (find-files "dist" "\\.whl$")))) | |
853 | (invoke "pip" "--no-cache-dir" "--no-input" | |
854 | "install" "--no-deps" "--prefix" #$output whl))))))) | |
855 | (native-inputs (list python-pypa-build python-flit-core python-pytest)) | |
856 | (propagated-inputs (list gmsh python-meshio python-numpy)) | |
3af31bc2 PG |
857 | (home-page "https://github.com/nschloe/pygmsh") |
858 | (synopsis "Python frontend for Gmsh") | |
859 | (description "The goal of @code{pygmsh} is to combine the power of | |
860 | Gmsh with the versatility of Python. The package generalises many of | |
861 | the methods and functions that comprise the Gmsh Python API. In this | |
862 | way the meshing of complex geometries using high-level abstractions is | |
863 | made possible. The package provides a Python library together with a | |
864 | command-line utility for mesh optimisation.") | |
5125d005 | 865 | (license license:gpl3+))) |
b05a1eb5 PG |
866 | |
867 | (define-public python-dolfin-adjoint | |
868 | (package | |
869 | (name "python-dolfin-adjoint") | |
870 | (version "2019.1.0") | |
871 | (source | |
872 | (origin | |
873 | (method git-fetch) | |
874 | (uri (git-reference | |
875 | (url "https://github.com/dolfin-adjoint/pyadjoint") | |
876 | (commit version))) | |
877 | (file-name (git-file-name name version)) | |
878 | (sha256 | |
879 | (base32 | |
880 | "0xhy76a5f33hz94wc9g2mc5qmwkxfccbbc6yxl7psm130afp8lhn")) | |
881 | (modules '((guix build utils))) | |
882 | (snippet | |
883 | '(begin | |
884 | ;; One of the migration tests attempts to call openmpi | |
885 | ;; recursively and fails. See | |
886 | ;; https://bitbucket.org/mpi4py/mpi4py/issues/95. Run the | |
887 | ;; test sequentially instead. | |
888 | (with-directory-excursion "tests/migration/optimal_control_mms" | |
889 | (substitute* "test_optimal_control_mms.py" | |
890 | (("\\\"mpirun\\\", \\\"-n\\\", \\\"2\\\", ") ""))) | |
891 | ;; Result files are regenerated in the check phase. | |
892 | (delete-file-recursively | |
893 | "tests/migration/viscoelasticity/test-results") | |
894 | #t)))) | |
895 | (build-system python-build-system) | |
896 | (inputs | |
8394619b | 897 | (list fenics openmpi pybind11)) |
b05a1eb5 | 898 | (native-inputs |
8394619b LC |
899 | (list pkg-config |
900 | python-coverage | |
901 | python-decorator | |
902 | python-flake8 | |
903 | python-pkgconfig | |
904 | python-pytest)) | |
b05a1eb5 PG |
905 | (propagated-inputs |
906 | `(("scipy" ,python-scipy))) | |
907 | (arguments | |
908 | `(#:phases | |
909 | (modify-phases %standard-phases | |
910 | (add-after 'build 'mpi-setup | |
911 | ,%openmpi-setup) | |
912 | (add-after 'install 'install-doc | |
913 | (lambda* (#:key outputs #:allow-other-keys) | |
914 | (let* ((doc (string-append (assoc-ref outputs "out") | |
915 | "/share/doc/" ,name "-" | |
916 | ,version)) | |
917 | (examples (string-append doc "/examples"))) | |
918 | (mkdir-p examples) | |
919 | (copy-recursively "examples" examples)) | |
920 | #t)) | |
921 | (replace 'check | |
922 | (lambda* (#:key inputs outputs tests? #:allow-other-keys) | |
923 | (when tests? | |
924 | (add-installed-pythonpath inputs outputs) | |
925 | (setenv "HOME" (getcwd)) | |
926 | (and (invoke "py.test" "-v" "tests/fenics_adjoint") | |
927 | (invoke "py.test" "-v" "tests/migration") | |
928 | (invoke "py.test" "-v" "tests/pyadjoint"))) | |
929 | #t))))) | |
930 | (home-page "http://www.dolfin-adjoint.org") | |
931 | (synopsis "Automatic differentiation library") | |
932 | (description "@code{python-dolfin-adjoint} is a solver of | |
933 | differential equations associated with a governing system and a | |
934 | functional of interest. Working from the forward model the solver | |
935 | automatically derives the discrete adjoint and tangent linear models. | |
936 | These additional models are key ingredients in many algorithms such as | |
937 | data assimilation, optimal control, sensitivity analysis, design | |
938 | optimisation and error estimation. The dolfin-adjoint project | |
939 | provides the necessary tools and data structures for cases where the | |
940 | forward model is implemented in @code{fenics} or | |
941 | @url{https://firedrakeproject.org,firedrake}.") | |
942 | (license license:lgpl3))) |