neuron: 7.5 -> 8.2.1

    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";

{ 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>"

    done

  '';

  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

  ];

  enableParallelBuilding = true;

  patches = [ ./neuron_darwin_rpath.patch ];

  ## 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}"

  # 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

  '';

  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"]);

  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 = 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

  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

  '';

  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;

  };

}

--- 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; \

--- 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

{ 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;

  };

}