123 lines
3 KiB
Nix
123 lines
3 KiB
Nix
{
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lib,
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stdenv,
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fetchFromGitHub,
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readline,
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xorg,
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mpi,
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cmake,
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bison,
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flex,
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git,
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perl,
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gsl,
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xcbuild,
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python3,
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useMpi ? false,
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useIv ? true,
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useCore ? false,
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useRx3d ? false,
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}:
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let
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inherit (lib.lists) optionals;
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inherit (lib.strings) cmakeBool;
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in
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stdenv.mkDerivation (finalAttrs: {
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pname = "neuron";
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version = "8.2.6";
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# format is for pythonModule conversion
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format = "other";
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nativeBuildInputs =
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[
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cmake
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bison
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flex
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git
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]
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++ optionals useCore [
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perl
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gsl
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]
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++ optionals stdenv.hostPlatform.isDarwin [ xcbuild ];
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buildInputs = optionals useIv [
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xorg.libX11.dev
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xorg.libXcomposite.dev
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xorg.libXext.dev
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];
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propagatedBuildInputs =
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[
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readline
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python3
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python3.pkgs.wheel
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python3.pkgs.setuptools
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python3.pkgs.scikit-build
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python3.pkgs.matplotlib
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]
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++ optionals useMpi [
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mpi
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]
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++ optionals useMpi [
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python3.pkgs.mpi4py
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]
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++ optionals useRx3d [
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python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.6
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python3.pkgs.numpy
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];
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# Patch build shells for cmake (bin, src, cmake) and submodules (external)
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postPatch = ''
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patchShebangs ./bin ./src ./external ./cmake
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substituteInPlace external/coreneuron/extra/nrnivmodl_core_makefile.in \
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--replace-fail \
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"DESTDIR =" \
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"DESTDIR = $out"
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'';
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cmakeFlags = [
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(cmakeBool "NRN_ENABLE_INTERVIEWS" useIv)
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(cmakeBool "NRN_ENABLE_MPI" useMpi)
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(cmakeBool "NRN_ENABLE_CORENEURON" useCore)
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(cmakeBool "NRN_ENABLE_RX3D" useRx3d)
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];
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postInstall = ''
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mkdir -p $out/${python3.sitePackages}
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mv $out/lib/python/* $out/${python3.sitePackages}/
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rm -rf $out/lib/python build
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for entry in $out/lib/*.so; do
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# remove references to build
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patchelf --set-rpath $(patchelf --print-rpath $entry | tr ':' '\n' | sed '/^\/build/d' | tr '\n' ':') $entry
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done
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'';
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src = fetchFromGitHub {
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owner = "neuronsimulator";
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repo = "nrn";
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rev = finalAttrs.version;
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fetchSubmodules = true;
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hash = "sha256-xASBpsF8rIzrb5G+4Qi6rvWC2wqL7nAGlSeMsBAI6WM=";
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};
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meta = with lib; {
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description = "Simulation environment for empirically-based simulations of neurons and networks of neurons";
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longDescription = ''
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NEURON is a simulation environment for developing and exercising models of
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neurons and networks of neurons. It is particularly well-suited to problems where
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cable properties of cells play an important role, possibly including extracellular
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potential close to the membrane), and where cell membrane properties are complex,
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involving many ion-specific channels, ion accumulation, and second messengers
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'';
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sourceProvenance = with sourceTypes; [ fromSource ];
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license = licenses.bsd3;
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homepage = "http://www.neuron.yale.edu/neuron";
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maintainers = with maintainers; [
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adev
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davidcromp
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];
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platforms = platforms.all;
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};
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})
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