petsc: refactor and add petsc4py support (#379406)

diff --git a/config/BuildSystem/config/packages/petsc4py.py b/config/BuildSystem/config/packages/petsc4py.py

index 4a58243..831aa04 100644

--- a/config/BuildSystem/config/packages/petsc4py.py

+++ b/config/BuildSystem/config/packages/petsc4py.py

@@ -37,7 +37,7 @@ class Configure(config.package.Package):

   def Install(self):

     import os

-    installLibPath = os.path.join(self.installDir, 'lib')

+    installLibPath = os.path.join(self.installDir, 'lib', '@PYTHON_SITEPACKAGES@')

     if self.setCompilers.isDarwin(self.log):

       apple = 'You may need to\n (csh/tcsh) setenv MACOSX_DEPLOYMENT_TARGET 10.X\n (sh/bash) MACOSX_DEPLOYMENT_TARGET=10.X; export MACOSX_DEPLOYMENT_TARGET\nbefore running make on PETSc'

     else:

@@ -70,7 +70,7 @@ class Configure(config.package.Package):

       newdir += 'NUMPY_INCLUDE="'+numpy_include+'" '

     self.addDefine('HAVE_PETSC4PY',1)

-    self.addDefine('PETSC4PY_INSTALL_PATH','"'+os.path.join(self.installdir.dir,'lib')+'"')

+    self.addDefine('PETSC4PY_INSTALL_PATH','"'+installLibPath+'"')

     self.addMakeMacro('PETSC4PY','yes')

     self.addMakeRule('petsc4pybuild','', \

                        ['@echo "*** Building petsc4py ***"',\

  fetchzip,

  cctools,

  gfortran,

  replaceVars,

  python3,

  python3Packages,

  blas,

  lapack,

  mpiSupport ? true,

  zlib, # propagated by p4est but required by petsc

  mpi, # generic mpi dependency

  mpiCheckPhaseHook,

  petsc-withp4est ? false,

  hdf5-support ? false,

  hdf5,

  # Build options

  petsc-optimized ? true,

  petsc-scalar-type ? "real",

  petsc-precision ? "double",

  mpiSupport ? true,

  withPetsc4py ? false, # petsc python binding

  withFullDeps ? false, # full External libraries support

  # External libraries options

  withHdf5 ? true,

  withMetis ? withFullDeps,

  withParmetis ? false, # parmetis is unfree and should be enabled manualy

  withPtscotch ? withFullDeps,

  withScalapack ? withFullDeps,

  withMumps ? withFullDeps,

  withP4est ? withFullDeps,

  # External libraries

  hdf5-fortran-mpi,

  metis,

  parmetis,

  withParmetis ? false,

  scotch,

  scalapack,

  mumps_par,

  pkg-config,

  p4est,

  zlib, # propagated by p4est but required by petsc

  petsc-optimized ? false,

  petsc-scalar-type ? "real",

  petsc-precision ? "double",

}:

# This version of PETSc does not support a non-MPI p4est build

assert petsc-withp4est -> p4est.mpiSupport;

assert withP4est -> (p4est.mpiSupport && mpiSupport);

# Package parmetis depend on metis and mpi support

assert withParmetis -> (withMetis && mpiSupport);

assert withPtscotch -> mpiSupport;

assert withScalapack -> mpiSupport;

assert withMumps -> withScalapack;

stdenv.mkDerivation rec {

  pname = "petsc";

  };

  strictDeps = true;

  nativeBuildInputs = [

  nativeBuildInputs =

    [

      python3

      gfortran

      pkg-config

  ] ++ lib.optional mpiSupport mpi;

  buildInputs = [

    ]

    ++ lib.optional mpiSupport mpi

    ++ lib.optionals withPetsc4py [

      python3Packages.setuptools

      python3Packages.cython

    ];

  buildInputs =

    [

      blas

      lapack

  ] ++ lib.optional hdf5-support hdf5 ++ lib.optional petsc-withp4est p4est ++ lib.optionals withParmetis [ metis parmetis ];

    ]

    ++ lib.optional withHdf5 hdf5-fortran-mpi

    ++ lib.optional withP4est p4est

    ++ lib.optional withMetis metis

    ++ lib.optional withParmetis parmetis

    ++ lib.optional withPtscotch scotch

    ++ lib.optional withScalapack scalapack

    ++ lib.optional withMumps mumps_par;

  prePatch = lib.optionalString stdenv.hostPlatform.isDarwin ''

  propagatedBuildInputs = lib.optional withPetsc4py python3Packages.numpy;

  patches = [

    (replaceVars ./fix-petsc4py-install-prefix.patch {

      PYTHON_SITEPACKAGES = python3.sitePackages;

    })

  ];

  postPatch =

    ''

      patchShebangs ./lib/petsc/bin

    ''

    + lib.optionalString stdenv.hostPlatform.isDarwin ''

      substituteInPlace config/install.py \

        --replace /usr/bin/install_name_tool ${cctools}/bin/install_name_tool

    '';

  configureFlags = [

  configureFlags =

    [

      "--with-blas=1"

      "--with-lapack=1"

      "--with-scalar-type=${petsc-scalar-type}"

      "--with-precision=${petsc-precision}"

      "--with-mpi=${if mpiSupport then "1" else "0"}"

  ] ++ lib.optionals mpiSupport [

    ]

    ++ lib.optional withPetsc4py "--with-petsc4py=1"

    ++ lib.optionals mpiSupport [

      "--CC=mpicc"

      "--with-cxx=mpicxx"

      "--with-fc=mpif90"

  ] ++ lib.optionals (mpiSupport && withParmetis) [

    ]

    ++ lib.optionals withMetis [

      "--with-metis=1"

      "--with-metis-dir=${metis}"

    ]

    ++ lib.optionals withParmetis [

      "--with-parmetis=1"

      "--with-parmetis-dir=${parmetis}"

  ] ++ lib.optionals petsc-optimized [

    ]

    ++ lib.optionals withPtscotch [

      "--with-ptscotch=1"

      "--with-ptscotch-include=${lib.getDev scotch}/include"

      "--with-ptscotch-lib=[-L${lib.getLib scotch}/lib,-lptscotch,-lptesmumps,-lptscotchparmetisv3,-lptscotcherr,-lesmumps,-lscotch,-lscotcherr]"

    ]

    ++ lib.optionals withScalapack [

      "--with-scalapack=1"

      "--with-scalapack-dir=${scalapack}"

    ]

    ++ lib.optionals withMumps [

      "--with-mumps=1"

      "--with-mumps-dir=${mumps_par}"

    ]

    ++ lib.optionals withP4est [

      "--with-p4est=1"

      "--with-zlib-include=${lib.getDev zlib}/include"

      "--with-zlib-lib=[-L${lib.getLib zlib}/lib,-lz]"

    ]

    ++ lib.optionals withHdf5 [

      "--with-hdf5=1"

      "--with-hdf5-fortran-bindings=1"

      "--with-hdf5-include=${lib.getDev hdf5-fortran-mpi}/include"

      "--with-hdf5-lib=[-L${lib.getLib hdf5-fortran-mpi}/lib,-lhdf5]"

    ]

    ++ lib.optionals petsc-optimized [

      "--with-debugging=0"

      "COPTFLAGS=-O3"

      "FOPTFLAGS=-O3"

      "CXXOPTFLAGS=-O3"

      "CXXFLAGS=-O3"

    ];

  preConfigure = ''

    patchShebangs ./lib/petsc/bin

  '' + lib.optionalString petsc-withp4est ''

    configureFlagsArray+=(

      "--with-p4est=1"

      "--with-zlib-include=${zlib.dev}/include"

      "--with-zlib-lib=-L${zlib}/lib -lz"

    )

  '' + lib.optionalString hdf5-support ''

    configureFlagsArray+=(

      "--with-hdf5=1"

      "--with-hdf5-fortran-bindings=1"

      "--with-hdf5-include=${hdf5.dev}/include"

      "--with-hdf5-lib=-L${hdf5}/lib -lhdf5"

    )

  '';

  hardeningDisable = lib.optionals (!petsc-optimized) [

    "fortify"

  ### SCIENCE/PROGRAMMING

  ### SCIENCE/GEOLOGY

  pflotran = callPackage ../by-name/pf/pflotran/package.nix {

    petsc = petsc.override {

      hdf5-support = true;

      hdf5 = hdf5-fortran-mpi;

      petsc-optimized = true;

    };

  };

  ### SCIENCE/LOGIC

  abella = callPackage ../applications/science/logic/abella {

  pesq = callPackage ../development/python-modules/pesq { };

  petsc4py = toPythonModule (pkgs.petsc.override {

    python3 = python;

    python3Packages = self;

    withPetsc4py = true;

    withFullDeps = true;

  });

  pex = callPackage ../development/python-modules/pex { };

  pexif = callPackage ../development/python-modules/pexif { };