nixpkgs/pkgs/applications/science/biology/nest/default.nix

{
  lib,
  stdenv,
  fetchFromGitHub,
  testers,
  cmake,
  gsl,
  libtool,
  findutils,
  llvmPackages,
  mpi,
  nest,
  pkg-config,
  boost,
  python3,
  readline,
  withPython ? false,
  withMpi ? false,
}:

stdenv.mkDerivation rec {
  pname = "nest";
  version = "3.8";

  src = fetchFromGitHub {
    owner = "nest";
    repo = "nest-simulator";
    rev = "v${version}";
    hash = "sha256-hysOe1ZZpCClVOGo0+UeCP7imAakXrZlnJ4V95zfiyA=";
  };

  postPatch = ''
    patchShebangs cmake/CheckFiles/check_return_val.sh
    # fix PyNEST installation path
    # it expects CMAKE_INSTALL_LIBDIR to be relative
    substituteInPlace cmake/ProcessOptions.cmake \
      --replace "\''${CMAKE_INSTALL_LIBDIR}/python" "lib/python"
  '';

  nativeBuildInputs = [
    cmake
    pkg-config
    findutils
  ];

  buildInputs =
    [
      gsl
      readline
      libtool # libltdl
      boost
    ]
    ++ lib.optionals withPython [
      python3
      python3.pkgs.cython
    ]
    ++ lib.optional withMpi mpi
    ++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp;

  propagatedBuildInputs = with python3.pkgs; [
    numpy
  ];

  cmakeFlags = [
    "-Dwith-python=${if withPython then "ON" else "OFF"}"
    "-Dwith-mpi=${if withMpi then "ON" else "OFF"}"
    "-Dwith-openmp=ON"
  ];

  postInstall = ''
    # Alternative to autoPatchElf, moves libraries where
    # Nest expects them to be
    find $out/lib/nest -exec ln -s {} $out/lib \;
  '';

  passthru.tests.version = testers.testVersion {
    package = nest;
    command = "nest --version";
  };

  meta = {
    description = "Command line tool for simulating neural networks";
    homepage = "https://www.nest-simulator.org/";
    changelog = "https://github.com/nest/nest-simulator/releases/tag/v${version}";
    license = lib.licenses.gpl2Plus;
    maintainers = with lib.maintainers; [
      jiegec
      davidcromp
    ];
    platforms = lib.platforms.unix;
  };
}