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{ lib, stdenv
, fetchurl
, pkg-config
, automake
, autoconf
, libtool
, ncurses
, readline
, which
, python ? null
, useMpi ? false
, mpi
, iv
}:
stdenv.mkDerivation rec {
pname = "neuron${lib.optionalString useMpi "-mpi"}";
version = "7.5";
nativeBuildInputs = [ which pkg-config automake autoconf libtool ];
buildInputs = [ ncurses readline python iv ]
++ lib.optional useMpi mpi;
src = fetchurl {
url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz";
sha256 = "0f26v3qvzblcdjg7isq0m9j2q8q7x3vhmkfllv8lsr3gyj44lljf";
};
patches = (lib.optional (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]);
# With LLVM 3.8 and above, clang (really libc++) gets upset if you attempt to redefine these...
postPatch = lib.optionalString stdenv.cc.isClang ''
substituteInPlace src/gnu/neuron_gnu_builtin.h \
--replace 'double abs(double arg);' "" \
--replace 'float abs(float arg);' "" \
--replace 'short abs(short arg);' "" \
--replace 'long abs(long arg);' ""
'' + lib.optionalString stdenv.isDarwin ''
# we are darwin, but we don't have all the quirks the source wants to compensate for
substituteInPlace src/nrnpython/setup.py.in --replace 'readline="edit"' 'readline="readline"'
for f in src/nrnpython/*.[ch] ; do
substituteInPlace $f --replace "<Python/Python.h>" "<Python.h>"
done
'';
enableParallelBuilding = true;
## neuron install by default everything under prefix/${host_arch}/*
## override this to support nix standard file hierarchy
## without issues: install everything under prefix/
preConfigure = ''
./build.sh
export prefix="''${prefix} --exec-prefix=''${out}"
'';
configureFlags = with lib;
[ "--with-readline=${readline}" "--with-iv=${iv}" ]
++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ]
++ (if useMpi then ["--with-mpi" "--with-paranrn"]
else ["--without-mpi"]);
postInstall = lib.optionalString (python != null) ''
## standardise python neuron install dir if any
if [[ -d $out/lib/python ]]; then
mkdir -p ''${out}/${python.sitePackages}
mv ''${out}/lib/python/* ''${out}/${python.sitePackages}/
fi
'';
propagatedBuildInputs = [ readline ncurses which libtool ];
meta = with lib; {
broken = stdenv.isDarwin;
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";
license = licenses.bsd3;
homepage = "http://www.neuron.yale.edu/neuron";
maintainers = [ maintainers.adev ];
# source claims it's only tested for x86 and powerpc
platforms = platforms.x86_64 ++ platforms.i686;
};
}
|
