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{ lib
, stdenv
, fetchFromGitHub
, readline
, xorg
, mpi
, cmake
, bison
, flex
, git
, perl
, gsl
, xcbuild
, python3
, useMpi ? false
, useIv ? true
, useCore ? false
, useRx3d ? false
}:
let
inherit (lib.lists) optionals;
inherit (lib.strings) cmakeBool;
in
stdenv.mkDerivation (finalAttrs: {
pname = "neuron";
version = "8.2.4";
# format is for pythonModule conversion
format = "other";
nativeBuildInputs = [
cmake
bison
flex
git
] ++ optionals useCore [ perl gsl ]
++ optionals stdenv.isDarwin [ xcbuild ];
buildInputs = optionals useIv [
xorg.libX11.dev
xorg.libXcomposite.dev
xorg.libXext.dev
];
propagatedBuildInputs = [
readline
python3
python3.pkgs.wheel
python3.pkgs.setuptools
python3.pkgs.scikit-build
python3.pkgs.matplotlib
] ++ optionals useMpi [
mpi
] ++ optionals useMpi [
python3.pkgs.mpi4py
] ++ optionals useRx3d [
python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.4
python3.pkgs.numpy
];
# Patch build shells for cmake (bin, src, cmake) and submodules (external)
postPatch = ''
patchShebangs ./bin ./src ./external ./cmake
substituteInPlace external/coreneuron/extra/nrnivmodl_core_makefile.in \
--replace-fail \
"DESTDIR =" \
"DESTDIR = $out"
'';
cmakeFlags = [
(cmakeBool "NRN_ENABLE_INTERVIEWS" useIv)
(cmakeBool "NRN_ENABLE_MPI" useMpi)
(cmakeBool "NRN_ENABLE_CORENEURON" useCore)
(cmakeBool "NRN_ENABLE_RX3D" useRx3d)
];
postInstall = ''
mkdir -p $out/${python3.sitePackages}
mv $out/lib/python/* $out/${python3.sitePackages}/
rm -rf $out/lib/python build
for entry in $out/lib/*.so; do
# remove references to build
patchelf --set-rpath $(patchelf --print-rpath $entry | tr ':' '\n' | sed '/^\/build/d' | tr '\n' ':') $entry
done
'';
src = fetchFromGitHub {
owner = "neuronsimulator";
repo = "nrn";
rev = finalAttrs.version;
fetchSubmodules = true;
hash = "sha256-KsULc+LHoWmrkGYebpoUot6DhStKidbLQf5a3S+pi4s=";
};
meta = with lib; {
description = "Simulation environment for empirically-based simulations of neurons and networks of neurons";
longDescription = ''
NEURON is a simulation environment for developing and exercising models of
neurons and networks of neurons. It is particularly well-suited to problems where
cable properties of cells play an important role, possibly including extracellular
potential close to the membrane), and where cell membrane properties are complex,
involving many ion-specific channels, ion accumulation, and second messengers
'';
sourceProvenance = with sourceTypes; [ fromSource ];
license = licenses.bsd3;
homepage = "http://www.neuron.yale.edu/neuron";
maintainers = with maintainers; [ adev davidcromp ];
platforms = platforms.all;
};
})
|
