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

maintainers/maintainer-list.nix

@@ -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";

pkgs/applications/science/biology/neuron/default.nix

@@ -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
-                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
-    ];
-    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;
+    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 ];
+    license = licenses.bsd3;
+    homepage = "http://www.neuron.yale.edu/neuron";
+    maintainers = with maintainers; [ adev davidcromp ];
+    platforms = platforms.all;
   };
 }

pkgs/applications/science/biology/neuron/neuron-carbon-disable.patch

@@ -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; \

pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch

@@ -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

pkgs/development/python-modules/neuronpy/default.nix

@@ -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;
-  };
-
-}

pkgs/top-level/all-packages.nix

@@ -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 { };
 

pkgs/top-level/python-packages.nix

@@ -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 { };