pkgs/development/python-modules/fenics/default.nix

   1 {
   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,
  31 }:
  32
  33 let
  34   version = "2019.1.0";
  35
  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   };
  63
  64   fiat = pythonPackages.buildPythonPackage {
  65     pname = "fiat";
  66     inherit version;
  67     src = fetchurl {
  68       url = "https://bitbucket.org/fenics-project/fiat/downloads/fiat-${version}.tar.gz";
  69       sha256 = "1sbi0fbr7w9g9ajr565g3njxrc3qydqjy3334vmz5xg0rd3106il";
  70     };
  71     propagatedBuildInputs = [
  72       numpy
  73       six
  74       sympy
  75     ];
  76     nativeCheckInputs = [ pytest ];
  77
  78     preCheck = ''
  79       # Workaround pytest 4.6.3 issue.
  80       # See: https://bitbucket.org/fenics-project/fiat/pull-requests/59
  81       rm test/unit/test_quadrature.py
  82       rm test/unit/test_reference_element.py
  83       rm test/unit/test_fiat.py
  84
  85       # Fix `np.float` deprecation in Numpy 1.20
  86       grep -lr 'np.float(' test/ | while read -r fn; do
  87         substituteInPlace "$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   };
 103
 104   ufl = pythonPackages.buildPythonPackage {
 105     pname = "ufl";
 106     inherit version;
 107     src = fetchurl {
 108       url = "https://bitbucket.org/fenics-project/ufl/downloads/ufl-${version}.tar.gz";
 109       sha256 = "04daxwg4y9c51sdgvwgmlc82nn0fjw7i2vzs15ckdc7dlazmcfi1";
 110     };
 111     propagatedBuildInputs = [
 112       numpy
 113       six
 114     ];
 115     nativeCheckInputs = [ pytest ];
 116     checkPhase = ''
 117       runHook preCheck
 118       py.test test/
 119       runHook postCheck
 120     '';
 121     meta = {
 122       description = "Domain-specific language for finite element variational forms";
 123       homepage = "https://fenicsproject.org/";
 124       platforms = lib.platforms.all;
 125       license = lib.licenses.lgpl3;
 126     };
 127   };
 128
 129   ffc = pythonPackages.buildPythonPackage {
 130     pname = "ffc";
 131     inherit version;
 132     src = fetchurl {
 133       url = "https://bitbucket.org/fenics-project/ffc/downloads/ffc-${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     ];
 270
 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   };
 291 in
 292 python-dolfin