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