pyrox.dev
1{
2 lib,
3 stdenv,
4 fetchurl,
5 fetchpatch,
6 blas,
7 boost186,
8 buildPythonPackage,
9 cmake,
10 doxygen,
11 eigen,
12 hdf5,
13 isPy27,
14 lapack,
15 mpi,
16 mpi4py,
17 numpy,
18 pkg-config,
19 pkgconfig,
20 ply,
21 pybind11,
22 pytest,
23 python,
24 scotch,
25 setuptools,
26 six,
27 sphinx,
28 suitesparse,
29 swig,
30 sympy,
31 zlib,
32 nixosTests,
33}:
34
35let
36 version = "2019.1.0";
37
38 dijitso = buildPythonPackage {
39 pname = "dijitso";
40 inherit version;
41 src = fetchurl {
42 url = "https://bitbucket.org/fenics-project/dijitso/downloads/dijitso-${version}.tar.gz";
43 sha256 = "1ncgbr0bn5cvv16f13g722a0ipw6p9y6p4iasxjziwsp8kn5x97a";
44 };
45 propagatedBuildInputs = [
46 numpy
47 six
48 ];
49 nativeCheckInputs = [ pytest ];
50 preCheck = ''
51 export HOME=$PWD
52 '';
53 checkPhase = ''
54 runHook preCheck
55 py.test test/
56 runHook postCheck
57 '';
58 meta = {
59 description = "Distributed just-in-time shared library building";
60 homepage = "https://fenicsproject.org/";
61 platforms = lib.platforms.all;
62 license = lib.licenses.lgpl3;
63 };
64 };
65
66 fiat = buildPythonPackage {
67 pname = "fiat";
68 inherit version;
69 src = fetchurl {
70 url = "https://bitbucket.org/fenics-project/fiat/downloads/fiat-${version}.tar.gz";
71 sha256 = "1sbi0fbr7w9g9ajr565g3njxrc3qydqjy3334vmz5xg0rd3106il";
72 };
73 propagatedBuildInputs = [
74 numpy
75 six
76 sympy
77 ];
78 nativeCheckInputs = [ pytest ];
79
80 preCheck = ''
81 # Workaround pytest 4.6.3 issue.
82 # See: https://bitbucket.org/fenics-project/fiat/pull-requests/59
83 rm test/unit/test_quadrature.py
84 rm test/unit/test_reference_element.py
85 rm test/unit/test_fiat.py
86
87 # Fix `np.float` deprecation in Numpy 1.20
88 grep -lr 'np.float(' test/ | while read -r fn; do
89 substituteInPlace "$fn" \
90 --replace "np.float(" "np.float64("
91 done
92 '';
93 checkPhase = ''
94 runHook preCheck
95 py.test test/unit/
96 runHook postCheck
97 '';
98 meta = {
99 description = "Automatic generation of finite element basis functions";
100 homepage = "https://fenicsproject.org/";
101 platforms = lib.platforms.all;
102 license = lib.licenses.lgpl3;
103 };
104 };
105
106 ufl = buildPythonPackage {
107 pname = "ufl";
108 inherit version;
109 src = fetchurl {
110 url = "https://bitbucket.org/fenics-project/ufl/downloads/ufl-${version}.tar.gz";
111 sha256 = "04daxwg4y9c51sdgvwgmlc82nn0fjw7i2vzs15ckdc7dlazmcfi1";
112 };
113 propagatedBuildInputs = [
114 numpy
115 six
116 ];
117 nativeCheckInputs = [ pytest ];
118 checkPhase = ''
119 runHook preCheck
120 py.test test/
121 runHook postCheck
122 '';
123 meta = {
124 description = "Domain-specific language for finite element variational forms";
125 homepage = "https://fenicsproject.org/";
126 platforms = lib.platforms.all;
127 license = lib.licenses.lgpl3;
128 };
129 };
130
131 ffc = buildPythonPackage {
132 pname = "ffc";
133 inherit version;
134 src = fetchurl {
135 url = "https://bitbucket.org/fenics-project/ffc/downloads/ffc-${version}.tar.gz";
136 sha256 = "1zdg6pziss4va74pd7jjl8sc3ya2gmhpypccmyd8p7c66ji23y2g";
137 };
138 patches = [
139 (fetchpatch {
140 name = "fenics-ffc-numpy2-compat.patch";
141 url = "https://bitbucket.org/fenics-project/ffc/commits/245d15115b35b5ac091251fe6c84cc6474704b3c/raw";
142 hash = "sha256-TcLQZ44C+uR2ryxtCBjR/5Tjn7B0S4MqoYi0nlP8JwI=";
143 })
144 ];
145 nativeBuildInputs = [ pybind11 ];
146 propagatedBuildInputs = [
147 dijitso
148 fiat
149 numpy
150 six
151 sympy
152 ufl
153 setuptools
154 ];
155 nativeCheckInputs = [ pytest ];
156 preCheck = ''
157 export HOME=$PWD
158 rm test/unit/ufc/finite_element/test_evaluate.py
159 '';
160 checkPhase = ''
161 runHook preCheck
162 py.test test/unit/
163 runHook postCheck
164 '';
165 meta = {
166 description = "Compiler for finite element variational forms";
167 homepage = "https://fenicsproject.org/";
168 platforms = lib.platforms.all;
169 license = lib.licenses.lgpl3;
170 };
171 };
172 dolfin = stdenv.mkDerivation {
173 pname = "dolfin";
174 inherit version;
175 src = fetchurl {
176 url = "https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-${version}.tar.gz";
177 sha256 = "0kbyi4x5f6j4zpasch0swh0ch81w2h92rqm1nfp3ydi4a93vky33";
178 };
179 patches = [
180 (fetchpatch {
181 name = "fix-double-prefix.patch";
182 url = "https://bitbucket.org/josef_kemetmueller/dolfin/commits/328e94acd426ebaf2243c072b806be3379fd4340/raw";
183 sha256 = "1zj7k3y7vsx0hz3gwwlxhq6gdqamqpcw90d4ishwx5ps5ckcsb9r";
184 })
185 (fetchpatch {
186 url = "https://bitbucket.org/fenics-project/dolfin/issues/attachments/1116/fenics-project/dolfin/1602778118.04/1116/0001-Use-__BYTE_ORDER__-instead-of-removed-Boost-endian.h.patch";
187 hash = "sha256-wPaDmPU+jaD3ce3nNEbvM5p8e3zBdLozamLTJ/0ai2c=";
188 })
189 (fetchpatch {
190 name = "fenics-boost-filesystem-1.85-compat.patch.";
191 url = "https://bitbucket.org/sblauth/dolfin/commits/16fa03887b3e9ec417c484ddf92db104cb9a93f9/raw";
192 hash = "sha256-ZMKfzeWlPre88cKzrj04Tj+nQWS4ixat0bBvyt3TJmk=";
193 })
194 ];
195 # https://aur.archlinux.org/cgit/aur.git/plain/PKGBUILD?h=dolfin&id=a965ad934f7b3d49a5e77fa6fb5e3c710ec2163e
196 postPatch = ''
197 sed -i '20 a #include <algorithm>' dolfin/geometry/IntersectionConstruction.cpp
198 sed -i '26 a #include <algorithm>' dolfin/mesh/MeshFunction.h
199 sed -i '25 a #include <cstdint>' dolfin/mesh/MeshConnectivity.h
200 '';
201 propagatedBuildInputs = [
202 dijitso
203 fiat
204 numpy
205 six
206 ufl
207 ];
208 nativeBuildInputs = [
209 cmake
210 doxygen
211 pkg-config
212 ];
213 buildInputs = [
214 boost186
215 dijitso
216 eigen
217 ffc
218 fiat
219 hdf5
220 mpi
221 numpy
222 blas
223 lapack
224 ply
225 python
226 scotch
227 six
228 sphinx
229 suitesparse
230 swig
231 sympy
232 ufl
233 zlib
234 ];
235 cmakeFlags = [
236 "-DDOLFIN_CXX_FLAGS=-std=c++11"
237 "-DDOLFIN_AUTO_DETECT_MPI=ON"
238 "-DDOLFIN_ENABLE_CHOLMOD=ON"
239 "-DDOLFIN_ENABLE_DOCS=ON"
240 "-DDOLFIN_ENABLE_HDF5=ON"
241 "-DDOLFIN_ENABLE_MPI=ON"
242 "-DDOLFIN_ENABLE_SCOTCH=ON"
243 "-DDOLFIN_ENABLE_UMFPACK=ON"
244 "-DDOLFIN_ENABLE_ZLIB=ON"
245 "-DDOLFIN_SKIP_BUILD_TESTS=ON" # Otherwise SCOTCH is not found
246 # TODO: Enable the following features
247 "-DDOLFIN_ENABLE_PARMETIS=OFF"
248 "-DDOLFIN_ENABLE_PETSC=OFF"
249 "-DDOLFIN_ENABLE_SLEPC=OFF"
250 "-DDOLFIN_ENABLE_TRILINOS=OFF"
251 ];
252 installCheckPhase = ''
253 source $out/share/dolfin/dolfin.conf
254 make runtests
255 '';
256 meta = {
257 description = "FEniCS Problem Solving Environment in Python and C++";
258 homepage = "https://fenicsproject.org/";
259 license = lib.licenses.lgpl3;
260 };
261 };
262 python-dolfin = buildPythonPackage rec {
263 pname = "dolfin";
264 inherit version;
265 disabled = isPy27;
266 src = dolfin.src;
267 sourceRoot = "${pname}-${version}/python";
268 nativeBuildInputs = [
269 pybind11
270 cmake
271 ];
272 dontUseCmakeConfigure = true;
273 preConfigure = ''
274 export CMAKE_PREFIX_PATH=${pybind11}/share/cmake/pybind11:$CMAKE_PREFIX_PATH
275 substituteInPlace setup.py --replace "pybind11==2.2.4" "pybind11"
276 substituteInPlace dolfin/jit/jit.py \
277 --replace 'pkgconfig.exists("dolfin")' 'pkgconfig.exists("${dolfin}/lib/pkgconfig/dolfin.pc")' \
278 --replace 'pkgconfig.parse("dolfin")' 'pkgconfig.parse("${dolfin}/lib/pkgconfig/dolfin.pc")'
279 '';
280 buildInputs = [
281 dolfin
282 boost186
283 ];
284
285 propagatedBuildInputs = [
286 dijitso
287 ffc
288 mpi4py
289 numpy
290 ufl
291 pkgconfig
292 pybind11
293 ];
294 doCheck = false; # Tries to orte_ess_init and call ssh to localhost
295 passthru.tests = {
296 inherit (nixosTests) fenics;
297 };
298 meta = {
299 description = "Python bindings for the DOLFIN FEM compiler";
300 homepage = "https://fenicsproject.org/";
301 platforms = lib.platforms.all;
302 license = lib.licenses.lgpl3;
303 };
304 };
305in
306python-dolfin