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

   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
  32 let
  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       (fetchpatch {
 168         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";
 169         hash = "sha256-wPaDmPU+jaD3ce3nNEbvM5p8e3zBdLozamLTJ/0ai2c=";
 170       })
 171     ];
 172     # https://aur.archlinux.org/cgit/aur.git/plain/PKGBUILD?h=dolfin&id=a965ad934f7b3d49a5e77fa6fb5e3c710ec2163e
 173     postPatch = ''
 174       sed -i '20 a #include <algorithm>' dolfin/geometry/IntersectionConstruction.cpp
 175       sed -i '26 a #include <algorithm>' dolfin/mesh/MeshFunction.h
 176       sed -i '25 a #include <cstdint>' dolfin/mesh/MeshConnectivity.h
 177     '';
 178     propagatedBuildInputs = [
 179       dijitso
 180       fiat
 181       numpy
 182       six
 183       ufl
 184     ];
 185     nativeBuildInputs = [
 186       cmake
 187       doxygen
 188       pkg-config
 189     ];
 190     buildInputs = [
 191       boost
 192       dijitso
 193       eigen
 194       ffc
 195       fiat
 196       hdf5
 197       mpi
 198       numpy
 199       blas
 200       lapack
 201       ply
 202       python
 203       scotch
 204       six
 205       sphinx
 206       suitesparse
 207       swig
 208       sympy
 209       ufl
 210       zlib
 211     ];
 212     cmakeFlags = [
 213       "-DDOLFIN_CXX_FLAGS=-std=c++11"
 214       "-DDOLFIN_AUTO_DETECT_MPI=ON"
 215       "-DDOLFIN_ENABLE_CHOLMOD=ON"
 216       "-DDOLFIN_ENABLE_DOCS=ON"
 217       "-DDOLFIN_ENABLE_HDF5=ON"
 218       "-DDOLFIN_ENABLE_MPI=ON"
 219       "-DDOLFIN_ENABLE_SCOTCH=ON"
 220       "-DDOLFIN_ENABLE_UMFPACK=ON"
 221       "-DDOLFIN_ENABLE_ZLIB=ON"
 222       "-DDOLFIN_SKIP_BUILD_TESTS=ON" # Otherwise SCOTCH is not found
 223       # TODO: Enable the following features
 224       "-DDOLFIN_ENABLE_PARMETIS=OFF"
 225       "-DDOLFIN_ENABLE_PETSC=OFF"
 226       "-DDOLFIN_ENABLE_SLEPC=OFF"
 227       "-DDOLFIN_ENABLE_TRILINOS=OFF"
 228     ];
 229     installCheckPhase = ''
 230       source $out/share/dolfin/dolfin.conf
 231       make runtests
 232     '';
 233     meta = {
 234       description = "The FEniCS Problem Solving Environment in Python and C++";
 235       homepage = "https://fenicsproject.org/";
 236       license = lib.licenses.lgpl3;
 237     };
 238   };
 239   python-dolfin = pythonPackages.buildPythonPackage rec {
 240     pname = "dolfin";
 241     inherit version;
 242     disabled = pythonPackages.isPy27;
 243     src = dolfin.src;
 244     sourceRoot = "${pname}-${version}/python";
 245     nativeBuildInputs = [
 246       pybind11
 247       cmake
 248     ];
 249     dontUseCmakeConfigure = true;
 250     preConfigure = ''
 251       export CMAKE_PREFIX_PATH=${pybind11}/share/cmake/pybind11:$CMAKE_PREFIX_PATH
 252       substituteInPlace setup.py --replace "pybind11==2.2.4" "pybind11"
 253       substituteInPlace dolfin/jit/jit.py \
 254         --replace 'pkgconfig.exists("dolfin")' 'pkgconfig.exists("${dolfin}/lib/pkgconfig/dolfin.pc")' \
 255         --replace 'pkgconfig.parse("dolfin")' 'pkgconfig.parse("${dolfin}/lib/pkgconfig/dolfin.pc")'
 256     '';
 257     buildInputs = [
 258       dolfin
 259       boost
 260     ];
 261
 262     propagatedBuildInputs = [
 263       dijitso
 264       ffc
 265       mpi4py
 266       numpy
 267       ufl
 268       pythonPackages.pkgconfig
 269       pythonPackages.pybind11
 270     ];
 271     doCheck = false; # Tries to orte_ess_init and call ssh to localhost
 272     passthru.tests = { inherit (nixosTests) fenics; };
 273     meta = {
 274       description = "Python bindings for the DOLFIN FEM compiler";
 275       homepage = "https://fenicsproject.org/";
 276       platforms = lib.platforms.all;
 277       license = lib.licenses.lgpl3;
 278     };
 279   };
 280 in python-dolfin