mirror of
https://github.com/NixOS/nixpkgs.git
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4f0dadbf38
After final improvements to the official formatter implementation,
this commit now performs the first treewide reformat of Nix files using it.
This is part of the implementation of RFC 166.
Only "inactive" files are reformatted, meaning only files that
aren't being touched by any PR with activity in the past 2 months.
This is to avoid conflicts for PRs that might soon be merged.
Later we can do a full treewide reformat to get the rest,
which should not cause as many conflicts.
A CI check has already been running for some time to ensure that new and
already-formatted files are formatted, so the files being reformatted here
should also stay formatted.
This commit was automatically created and can be verified using
nix-build a08b3a4d19.tar.gz \
--argstr baseRev b32a094368
result/bin/apply-formatting $NIXPKGS_PATH
124 lines
3.0 KiB
Nix
124 lines
3.0 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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