biome: 1.9.2 -> 1.9.3 (#349335)
[NixPkgs.git] / pkgs / development / python-modules / fenics / default.nix
blobb2750f7a7054c818370fee9190b9f09c27f85976
2   lib,
3   stdenv,
4   fetchurl,
5   fetchpatch,
6   blas,
7   boost,
8   cmake,
9   doxygen,
10   eigen,
11   hdf5,
12   lapack,
13   mpi,
14   mpi4py,
15   numpy,
16   pkg-config,
17   ply,
18   pybind11,
19   pytest,
20   python,
21   pythonPackages,
22   scotch,
23   setuptools,
24   six,
25   sphinx,
26   suitesparse,
27   swig,
28   sympy,
29   zlib,
30   nixosTests,
33 let
34   version = "2019.1.0";
36   dijitso = pythonPackages.buildPythonPackage {
37     pname = "dijitso";
38     inherit version;
39     src = fetchurl {
40       url = "https://bitbucket.org/fenics-project/dijitso/downloads/dijitso-${version}.tar.gz";
41       sha256 = "1ncgbr0bn5cvv16f13g722a0ipw6p9y6p4iasxjziwsp8kn5x97a";
42     };
43     propagatedBuildInputs = [
44       numpy
45       six
46     ];
47     nativeCheckInputs = [ pytest ];
48     preCheck = ''
49       export HOME=$PWD
50     '';
51     checkPhase = ''
52       runHook preCheck
53       py.test test/
54       runHook postCheck
55     '';
56     meta = {
57       description = "Distributed just-in-time shared library building";
58       homepage = "https://fenicsproject.org/";
59       platforms = lib.platforms.all;
60       license = lib.licenses.lgpl3;
61     };
62   };
64   fiat = pythonPackages.buildPythonPackage {
65     pname = "fiat";
66     inherit version;
67     src = fetchurl {
68       url = "https://bitbucket.org/fenics-project/fiat/downloads/fiat-${version}.tar.gz";
69       sha256 = "1sbi0fbr7w9g9ajr565g3njxrc3qydqjy3334vmz5xg0rd3106il";
70     };
71     propagatedBuildInputs = [
72       numpy
73       six
74       sympy
75     ];
76     nativeCheckInputs = [ pytest ];
78     preCheck = ''
79       # Workaround pytest 4.6.3 issue.
80       # See: https://bitbucket.org/fenics-project/fiat/pull-requests/59
81       rm test/unit/test_quadrature.py
82       rm test/unit/test_reference_element.py
83       rm test/unit/test_fiat.py
85       # Fix `np.float` deprecation in Numpy 1.20
86       grep -lr 'np.float(' test/ | while read -r fn; do
87         substituteInPlace "$fn" \
88           --replace "np.float(" "np.float64("
89       done
90     '';
91     checkPhase = ''
92       runHook preCheck
93       py.test test/unit/
94       runHook postCheck
95     '';
96     meta = {
97       description = "Automatic generation of finite element basis functions";
98       homepage = "https://fenicsproject.org/";
99       platforms = lib.platforms.all;
100       license = lib.licenses.lgpl3;
101     };
102   };
104   ufl = pythonPackages.buildPythonPackage {
105     pname = "ufl";
106     inherit version;
107     src = fetchurl {
108       url = "https://bitbucket.org/fenics-project/ufl/downloads/ufl-${version}.tar.gz";
109       sha256 = "04daxwg4y9c51sdgvwgmlc82nn0fjw7i2vzs15ckdc7dlazmcfi1";
110     };
111     propagatedBuildInputs = [
112       numpy
113       six
114     ];
115     nativeCheckInputs = [ pytest ];
116     checkPhase = ''
117       runHook preCheck
118       py.test test/
119       runHook postCheck
120     '';
121     meta = {
122       description = "Domain-specific language for finite element variational forms";
123       homepage = "https://fenicsproject.org/";
124       platforms = lib.platforms.all;
125       license = lib.licenses.lgpl3;
126     };
127   };
129   ffc = pythonPackages.buildPythonPackage {
130     pname = "ffc";
131     inherit version;
132     src = fetchurl {
133       url = "https://bitbucket.org/fenics-project/ffc/downloads/ffc-${version}.tar.gz";
134       sha256 = "1zdg6pziss4va74pd7jjl8sc3ya2gmhpypccmyd8p7c66ji23y2g";
135     };
136     nativeBuildInputs = [ pybind11 ];
137     propagatedBuildInputs = [
138       dijitso
139       fiat
140       numpy
141       six
142       sympy
143       ufl
144       setuptools
145     ];
146     nativeCheckInputs = [ pytest ];
147     preCheck = ''
148       export HOME=$PWD
149       rm test/unit/ufc/finite_element/test_evaluate.py
150     '';
151     checkPhase = ''
152       runHook preCheck
153       py.test test/unit/
154       runHook postCheck
155     '';
156     meta = {
157       description = "Compiler for finite element variational forms";
158       homepage = "https://fenicsproject.org/";
159       platforms = lib.platforms.all;
160       license = lib.licenses.lgpl3;
161     };
162   };
163   dolfin = stdenv.mkDerivation {
164     pname = "dolfin";
165     inherit version;
166     src = fetchurl {
167       url = "https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-${version}.tar.gz";
168       sha256 = "0kbyi4x5f6j4zpasch0swh0ch81w2h92rqm1nfp3ydi4a93vky33";
169     };
170     patches = [
171       (fetchpatch {
172         name = "fix-double-prefix.patch";
173         url = "https://bitbucket.org/josef_kemetmueller/dolfin/commits/328e94acd426ebaf2243c072b806be3379fd4340/raw";
174         sha256 = "1zj7k3y7vsx0hz3gwwlxhq6gdqamqpcw90d4ishwx5ps5ckcsb9r";
175       })
176       (fetchpatch {
177         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";
178         hash = "sha256-wPaDmPU+jaD3ce3nNEbvM5p8e3zBdLozamLTJ/0ai2c=";
179       })
180     ];
181     # https://aur.archlinux.org/cgit/aur.git/plain/PKGBUILD?h=dolfin&id=a965ad934f7b3d49a5e77fa6fb5e3c710ec2163e
182     postPatch = ''
183       sed -i '20 a #include <algorithm>' dolfin/geometry/IntersectionConstruction.cpp
184       sed -i '26 a #include <algorithm>' dolfin/mesh/MeshFunction.h
185       sed -i '25 a #include <cstdint>' dolfin/mesh/MeshConnectivity.h
186     '';
187     propagatedBuildInputs = [
188       dijitso
189       fiat
190       numpy
191       six
192       ufl
193     ];
194     nativeBuildInputs = [
195       cmake
196       doxygen
197       pkg-config
198     ];
199     buildInputs = [
200       boost
201       dijitso
202       eigen
203       ffc
204       fiat
205       hdf5
206       mpi
207       numpy
208       blas
209       lapack
210       ply
211       python
212       scotch
213       six
214       sphinx
215       suitesparse
216       swig
217       sympy
218       ufl
219       zlib
220     ];
221     cmakeFlags = [
222       "-DDOLFIN_CXX_FLAGS=-std=c++11"
223       "-DDOLFIN_AUTO_DETECT_MPI=ON"
224       "-DDOLFIN_ENABLE_CHOLMOD=ON"
225       "-DDOLFIN_ENABLE_DOCS=ON"
226       "-DDOLFIN_ENABLE_HDF5=ON"
227       "-DDOLFIN_ENABLE_MPI=ON"
228       "-DDOLFIN_ENABLE_SCOTCH=ON"
229       "-DDOLFIN_ENABLE_UMFPACK=ON"
230       "-DDOLFIN_ENABLE_ZLIB=ON"
231       "-DDOLFIN_SKIP_BUILD_TESTS=ON" # Otherwise SCOTCH is not found
232       # TODO: Enable the following features
233       "-DDOLFIN_ENABLE_PARMETIS=OFF"
234       "-DDOLFIN_ENABLE_PETSC=OFF"
235       "-DDOLFIN_ENABLE_SLEPC=OFF"
236       "-DDOLFIN_ENABLE_TRILINOS=OFF"
237     ];
238     installCheckPhase = ''
239       source $out/share/dolfin/dolfin.conf
240       make runtests
241     '';
242     meta = {
243       description = "FEniCS Problem Solving Environment in Python and C++";
244       homepage = "https://fenicsproject.org/";
245       license = lib.licenses.lgpl3;
246     };
247   };
248   python-dolfin = pythonPackages.buildPythonPackage rec {
249     pname = "dolfin";
250     inherit version;
251     disabled = pythonPackages.isPy27;
252     src = dolfin.src;
253     sourceRoot = "${pname}-${version}/python";
254     nativeBuildInputs = [
255       pybind11
256       cmake
257     ];
258     dontUseCmakeConfigure = true;
259     preConfigure = ''
260       export CMAKE_PREFIX_PATH=${pybind11}/share/cmake/pybind11:$CMAKE_PREFIX_PATH
261       substituteInPlace setup.py --replace "pybind11==2.2.4" "pybind11"
262       substituteInPlace dolfin/jit/jit.py \
263         --replace 'pkgconfig.exists("dolfin")' 'pkgconfig.exists("${dolfin}/lib/pkgconfig/dolfin.pc")' \
264         --replace 'pkgconfig.parse("dolfin")' 'pkgconfig.parse("${dolfin}/lib/pkgconfig/dolfin.pc")'
265     '';
266     buildInputs = [
267       dolfin
268       boost
269     ];
271     propagatedBuildInputs = [
272       dijitso
273       ffc
274       mpi4py
275       numpy
276       ufl
277       pythonPackages.pkgconfig
278       pythonPackages.pybind11
279     ];
280     doCheck = false; # Tries to orte_ess_init and call ssh to localhost
281     passthru.tests = {
282       inherit (nixosTests) fenics;
283     };
284     meta = {
285       description = "Python bindings for the DOLFIN FEM compiler";
286       homepage = "https://fenicsproject.org/";
287       platforms = lib.platforms.all;
288       license = lib.licenses.lgpl3;
289     };
290   };
292 python-dolfin