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Merge pull request #317310 from ConnorBaker/fix/python3Packages.neuronpy

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neuron: 8.2.3 -> 8.2.4; fixup
This commit is contained in:
Connor Baker 2024-06-05 15:32:01 -04:00 committed by GitHub
commit 4adc42b9d0
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2 changed files with 29 additions and 34 deletions
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52
pkgs/applications/science/biology/neuron/default.nix
View File

@ -1,6 +1,6 @@
{ lib
, stdenv
, fetchurl
, fetchFromGitHub
, readline
, xorg
, mpi
@ -17,11 +17,13 @@
, useCore ? false
, useRx3d ? false
}:
stdenv.mkDerivation rec {
let
inherit (lib.lists) optionals;
inherit (lib.strings) cmakeBool;
in
stdenv.mkDerivation (finalAttrs: {
pname = "neuron";
version = "8.2.3";
version = "8.2.4";
# format is for pythonModule conversion
format = "other";
@ -31,10 +33,10 @@ stdenv.mkDerivation rec {
bison
flex
git
] ++ lib.optionals useCore [ perl gsl ]
++ lib.optionals stdenv.isDarwin [ xcbuild ];
] ++ optionals useCore [ perl gsl ]
++ optionals stdenv.isDarwin [ xcbuild ];
buildInputs = lib.optionals useIv [
buildInputs = optionals useIv [
xorg.libX11.dev
xorg.libXcomposite.dev
xorg.libXext.dev
@ -47,28 +49,29 @@ stdenv.mkDerivation rec {
python3.pkgs.setuptools
python3.pkgs.scikit-build
python3.pkgs.matplotlib
] ++ lib.optionals useMpi [
] ++ optionals useMpi [
mpi
] ++ lib.optionals useMpi [
] ++ optionals useMpi [
python3.pkgs.mpi4py
] ++ lib.optionals useRx3d [
python3.pkgs.cython
] ++ optionals useRx3d [
python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.4
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
substituteInPlace external/coreneuron/extra/nrnivmodl_core_makefile.in \
--replace-fail \
"DESTDIR =" \
"DESTDIR = $out"
'';
cmakeFlags = [
"-DNRN_ENABLE_INTERVIEWS=${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=${if useRx3d then "ON" else "OFF"}"
(cmakeBool "NRN_ENABLE_INTERVIEWS" useIv)
(cmakeBool "NRN_ENABLE_MPI" useMpi)
(cmakeBool "NRN_ENABLE_CORENEURON" useCore)
(cmakeBool "NRN_ENABLE_RX3D" useRx3d)
];
postInstall = ''
@ -81,9 +84,12 @@ stdenv.mkDerivation rec {
done
'';
src = fetchurl {
url = "https://github.com/neuronsimulator/nrn/releases/download/${version}/full-src-package-${version}.tar.gz";
sha256 = "sha256-k8+71BRfh+a73sZho6v0QFRxVmrfx6jqrgaqammdtDI=";
src = fetchFromGitHub {
owner = "neuronsimulator";
repo = "nrn";
rev = finalAttrs.version;
fetchSubmodules = true;
hash = "sha256-KsULc+LHoWmrkGYebpoUot6DhStKidbLQf5a3S+pi4s=";
};
meta = with lib; {
@ -101,4 +107,4 @@ stdenv.mkDerivation rec {
maintainers = with maintainers; [ adev davidcromp ];
platforms = platforms.all;
};
}
})

11
pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch
View File

@ -1,11 +0,0 @@
--- 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