pyrox.dev
lol
neuron: fix on clang 3.8 and above
This is in preparation for upgrading Darwin stdenv to LLVM 4
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pkgs/applications/science/biology/neuron/default.nix
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pkgs/applications/science/biology/neuron/default.nix
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{ stdenv
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, fetchurl
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{ stdenv
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, fetchurl
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, pkgconfig
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, automake
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, autoconf
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, ncurses
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, readline
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, which
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, python ? null
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, python ? null
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, mpi ? null
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}:
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stdenv.mkDerivation rec {
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name = "neuron-${version}";
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version = "7.4";
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nativeBuildInputs = [ which pkgconfig automake autoconf libtool ];
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buildInputs = [ ncurses readline python mpi ];
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···
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patches = (stdenv.lib.optional (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]);
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# With LLVM 3.8 and above, clang (really libc++) gets upset if you attempt to redefine these...
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postPatch = stdenv.lib.optionalString stdenv.cc.isClang ''
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substituteInPlace src/gnu/neuron_gnu_builtin.h \
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--replace 'double abs(double arg);' "" \
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--replace 'float abs(float arg);' "" \
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--replace 'short abs(short arg);' "" \
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--replace 'long abs(long arg);' ""
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'';
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enableParallelBuilding = true;
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## neuron install by default everything under prefix/${host_arch}/*
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## override this to support nix standard file hierarchy
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## override this to support nix standard file hierarchy
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## without issues: install everything under prefix/
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preConfigure = ''
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./build.sh
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export prefix="''${prefix} --exec-prefix=''${out}"
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export prefix="''${prefix} --exec-prefix=''${out}"
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'';
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configureFlags = with stdenv.lib;
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[ "--without-x" "--with-readline=${readline}" ]
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++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ]
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++ (if mpi != null then ["--with-mpi" "--with-paranrn"]
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++ (if mpi != null then ["--with-mpi" "--with-paranrn"]
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else ["--without-mpi"]);
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postInstall = stdenv.lib.optionals (python != null) [ ''
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## standardise python neuron install dir if any
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if [[ -d $out/lib/python ]]; then
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mv ''${out}/lib/python/* ''${out}/${python.sitePackages}/
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fi
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''];
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propagatedBuildInputs = [ readline ncurses which libtool ];
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propagatedBuildInputs = [ readline ncurses which libtool ];
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meta = with stdenv.lib; {
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description = "Simulation environment for empirically-based simulations of neurons and networks of neurons";
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longDescription = "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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longDescription = "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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license = licenses.bsd3;
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homepage = http://www.neuron.yale.edu/neuron;
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maintainers = [ maintainers.adev ];
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platforms = platforms.all;
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};
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};
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}
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