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Merge pull request #198093 from DavidCromp/update/Neuron-and-python-bind

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Sandro 2023-02-21 22:04:47 +01:00 committed by GitHub
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7 changed files with 107 additions and 134 deletions
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6
maintainers/maintainer-list.nix
View file

@ -3404,6 +3404,12 @@
githubId = 6754950;
name = "David Armstrong Lewis";
};
davidcromp = {
email = "davidcrompton1192@gmail.com";
github = "DavidCromp";
githubId = 10701143;
name = "David Crompton";
};
davidrusu = {
email = "davidrusu.me@gmail.com";
github = "davidrusu";

152
pkgs/applications/science/biology/neuron/default.nix
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@ -1,94 +1,104 @@
{ lib, stdenv
{ lib
, stdenv
, fetchurl
, pkg-config
, automake
, autoconf
, libtool
, ncurses
, readline
, which
, python ? null
, useMpi ? false
, xorg
, mpi
, iv
, cmake
, bison
, flex
, git
, perl
, gsl
, xcbuild
, python3
, useMpi ? false
, useIv ? true
, useCore ? false
, useRx3d ? false
}:
stdenv.mkDerivation rec {
pname = "neuron${lib.optionalString useMpi "-mpi"}";
version = "7.5";
pname = "neuron";
version = "8.2.1";
nativeBuildInputs = [ which pkg-config automake autoconf libtool ];
buildInputs = [ ncurses readline python iv ]
++ lib.optional useMpi mpi;
# format is for pythonModule conversion
format = "other";
src = fetchurl {
url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz";
sha256 = "0f26v3qvzblcdjg7isq0m9j2q8q7x3vhmkfllv8lsr3gyj44lljf";
};
nativeBuildInputs = [
cmake
bison
flex
git
] ++ lib.optional useCore [ perl gsl ]
++ lib.optional stdenv.isDarwin [ xcbuild ];
patches = (lib.optionals (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]);
buildInputs = lib.optional useIv [
xorg.libX11.dev
xorg.libXcomposite.dev
xorg.libXext.dev
];
# 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 $f --replace "<Python/Python.h>" "<Python.h>"
propagatedBuildInputs = [
readline
python3
python3.pkgs.wheel
python3.pkgs.setuptools
python3.pkgs.scikit-build
python3.pkgs.matplotlib
] ++ lib.optional useMpi [
mpi
] ++ lib.optional useMpi [
python3.pkgs.mpi4py
] ++ lib.optional useRx3d [
python3.pkgs.cython
python3.pkgs.numpy
];
patches = [ ./neuron_darwin_rpath.patch ];
# Patch build shells for cmake (bin, src, cmake) and submodules (external)
postPatch = ''
patchShebangs ./bin ./src ./external ./cmake
sed -e 's#DESTDIR =#DESTDIR = '"$out"'#' -i external/coreneuron/extra/nrnivmodl_core_makefile.in
'';
cmakeFlags = [
"-DNRN_ENABLE_INTERVIEWS=${if useIv then "ON" else "OFF"}"
"-DNRN_ENABLE_MPI=${if useMpi then "ON" else "OFF"}"
"-DNRN_ENABLE_CORENEURON=${if useCore then "ON" else "OFF"}"
"-DNRN_ENABLE_RX3D=${if useRx3d then "ON" else "OFF"}"
];
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' ':') $entry
done
'';
enableParallelBuilding = true;
## neuron install by default everything under prefix/${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 ];
src = fetchurl {
url = "https://github.com/neuronsimulator/nrn/releases/download/${version}/full-src-package-${version}.tar.gz";
sha256 = "0kb0dn7nmivv3zflzkbj2fj3184zwp2crkxp0mdxkwm4kpnxqz0v";
};
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
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
] ++ lib.optionals (python != null) [
binaryNativeCode # "geometry3d" bundled libraries
];
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 = [ maintainers.adev ];
# source claims it's only tested for x86 and powerpc
platforms = platforms.x86_64 ++ platforms.i686;
maintainers = with maintainers; [ adev davidcromp ];
platforms = platforms.all;
};
}

21
pkgs/applications/science/biology/neuron/neuron-carbon-disable.patch
View file

@ -1,21 +0,0 @@
--- nrn-7.4/src/mac/Makefile.am 2015-11-12 21:42:45.000000000 +0100
+++ nrn-7.4.new/src/mac/Makefile.am 2016-08-24 17:43:39.000000000 +0200
@@ -15,18 +15,8 @@
host_cpu = @host_cpu@
if MAC_DARWIN
-carbon = @enable_carbon@
bin_SCRIPTS = $(launch_scripts)
install: install-am
-if UniversalMacBinary
- $(CC) -arch ppc -o aoutppc -Dcpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon
- $(CC) -arch i386 -o aouti386 -Dcpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon
- lipo aouti386 aoutppc -create -output a.out
-else
- gcc -g -arch i386 -Dncpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon
-
-endif
- carbon=$(carbon) sh $(srcdir)/launch_inst.sh "$(host_cpu)" "$(DESTDIR)$(prefix)" "$(srcdir)"
for i in $(S) ; do \
sed "s/^CPU.*/CPU=\"$(host_cpu)\"/" < $(DESTDIR)$(bindir)/$$i > temp; \
mv temp $(DESTDIR)$(bindir)/$$i; \

11
pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch Normal file
View file

@ -0,0 +1,11 @@
--- a/src/nrnpython/setup.py.in
+++ b/src/nrnpython/setup.py.in
@@ -124,7 +124,7 @@ libdirs = [destdir + get_escaped_path("@NRN_LIBDIR@"),
rpath_prefix_flag='-Wl,-R'
extra_link_args = [@NRN_LINK_FLAGS_COMMA_SEPARATED_STRINGS@]
@MAC_DARWIN_FALSE@extra_link_args += [rpath_prefix_flag+lib_path for lib_path in libdirs]
-@MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,@loader_path/../../")
+@MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,@loader_path/../../../")
@MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,%s" % ivlibdir)
# as neuron module will be built during make, add build/lib

31
pkgs/development/python-modules/neuronpy/default.nix
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@ -1,31 +0,0 @@
{ lib
, buildPythonPackage
, fetchPypi
, numpy
, matplotlib
, scipy
, isPy27
}:
buildPythonPackage rec {
pname = "neuronpy";
version = "0.1.6";
disabled = !isPy27;
src = fetchPypi {
inherit pname version;
sha256 = "1clhc2b5fy2l8nfrji4dagmj9419nj6kam090yqxhq5c28sngk25";
};
propagatedBuildInputs = [ numpy matplotlib scipy ];
#No tests included
doCheck = false;
meta = with lib; {
description = "Interfaces and utilities for the NEURON simulator and analysis of neural data";
maintainers = [ maintainers.nico202 ];
license = licenses.mit;
};
}

4
pkgs/top-level/all-packages.nix
View file

@ -36424,11 +36424,11 @@ with pkgs;
nest-mpi = callPackage ../applications/science/biology/nest { withMpi = true; };
neuron = callPackage ../applications/science/biology/neuron { python = null; };
neuron = callPackage ../applications/science/biology/neuron { };
neuron-mpi = neuron.override {useMpi = true; };
neuron-full = neuron-mpi.override { python = python2; };
neuron-full = neuron-mpi.override { useCore = true; useRx3d = true; };
mrbayes = callPackage ../applications/science/biology/mrbayes { };

6
pkgs/top-level/python-packages.nix
View file

@ -6334,11 +6334,9 @@ self: super: with self; {
networkx = callPackage ../development/python-modules/networkx { };
neuron-mpi = toPythonModule (pkgs.neuron-mpi.override { inherit python; });
neuron-full = pkgs.neuron-full.override { python3 = python; };
neuron = toPythonModule (pkgs.neuron.override { inherit python; });
neuronpy = callPackage ../development/python-modules/neuronpy { };
neuronpy = python.pkgs.toPythonModule neuron-full;
nevow = callPackage ../development/python-modules/nevow { };