Merge master into closure-size

The kde-5 stuff still didn't merge well.
I hand-fixed what I saw, but there may be more problems.

14 files changed, 220 insertions, 36 deletions

diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix
index e77e848bed2cd..7798b1bef6c10 100644
--- a/pkgs/applications/science/astronomy/stellarium/default.nix
+++ b/pkgs/applications/science/astronomy/stellarium/default.nix
@@ -1,14 +1,19 @@
-{ stdenv, fetchurl, cmake, freetype, libpng, mesa, gettext, openssl, qt5Full, perl, libiconv }:
+{ stdenv, fetchurl, cmake, freetype, libpng, mesa, gettext, openssl, perl, libiconv
+, qtscript, qtserialport, qttools
+}:
 
 stdenv.mkDerivation rec {
-  name = "stellarium-0.13.3";
+  name = "stellarium-0.14.2";
 
   src = fetchurl {
     url = "mirror://sourceforge/stellarium/${name}.tar.gz";
-    sha256 = "1ml6z2xda4vx61agdz54x8fw1b115gwc7rcy0zhz1jh6g5jvf0ij";
+    sha256 = "1xxil0rv61zc08znfv83cpsc47y1gjl2f3njhz0pn5zd8jpaa15a";
   };
 
-  buildInputs = [ cmake freetype libpng mesa gettext openssl perl libiconv qt5Full ];
+  buildInputs = [
+    cmake freetype libpng mesa gettext openssl perl libiconv qtscript
+    qtserialport qttools
+  ];
 
   enableParallelBuilding = true;
 
diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix
new file mode 100644
index 0000000000000..41813dcda1496
--- /dev/null
+++ b/pkgs/applications/science/biology/minc-tools/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, fetchurl, perl, cmake, flex, bison, libminc }:
+
+stdenv.mkDerivation rec {
+  _name = "minc-tools";
+  name  = "${_name}-2.3.00";
+
+  src = fetchurl {
+    url = "https://github.com/BIC-MNI/${_name}/archive/${_name}-2-3-00.tar.gz";
+    sha256 = "1d457vrwy2fl6ga2axnwn1cchkx2rmgixfzyb1zjxb06cxkfj1dm";
+  };
+
+  nativeBuildInputs = [ cmake flex bison ] ++ (if doCheck then [ perl ] else [ ]);
+  buildInputs = [ libminc ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
+
+  checkPhase = "ctest";
+  doCheck = true;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/BIC-MNI/minc-tools;
+    description = "Command-line utilities for working with MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix
new file mode 100644
index 0000000000000..33f6d50d8ad84
--- /dev/null
+++ b/pkgs/applications/science/biology/neuron/default.nix
@@ -0,0 +1,38 @@
+{ stdenv 
+, fetchurl 
+, pkgconfig 
+, ncurses 
+, mpi ? null
+}:
+
+stdenv.mkDerivation rec {
+  name = "neuron-7.4";
+  buildInputs = [ stdenv pkgconfig ncurses mpi ];
+
+  src = fetchurl {
+    url = "http://www.neuron.yale.edu/ftp/neuron/versions/v7.4/nrn-7.4.tar.gz";
+    sha256 = "1rid8cmv5mca0vqkgwahm0prkwkbdvchgw2bdwvx4adkn8bbl0ql";
+  };
+
+
+  enableParallelBuilding = true;
+
+  configureFlags = [ "--without-x"
+		     "${if mpi != null then "--with-mpi" else "--without-mpi"}" ];
+
+  meta = with stdenv.lib; {
+    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";
+
+    license     = licenses.bsd3;
+    homepage    = http://www.neuron.yale.edu/neuron;
+    maintainers = [ maintainers.adev ];
+    platforms   = platforms.all;
+  };  
+}
+
diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix
index 36c3b7e899dd8..32d39d8a609dc 100644
--- a/pkgs/applications/science/electronics/gtkwave/default.nix
+++ b/pkgs/applications/science/electronics/gtkwave/default.nix
@@ -1,10 +1,10 @@
 {stdenv, fetchurl, gtk, gperf, pkgconfig, bzip2, tcl, tk, judy, xz}:
 stdenv.mkDerivation rec {
-  name = "gtkwave-3.3.66";
+  name = "gtkwave-3.3.70";
 
   src = fetchurl {
     url = "mirror://sourceforge/gtkwave/${name}.tar.gz";
-    sha256 = "17mrmgr6zzl1x1qml0wmjjhcbw7bg3w4mqy60rsy0z6gxd8hikh4";
+    sha256 = "1akzf1sq8mwarrbrbz5chrvgwlsp444h5za8rg1dfyqk733s7piz";
   };
 
   buildInputs = [ gtk gperf pkgconfig bzip2 tcl tk judy xz ];
diff --git a/pkgs/applications/science/logic/eprover/default.nix b/pkgs/applications/science/logic/eprover/default.nix
index 97fe7065b85df..1f36858ae3208 100644
--- a/pkgs/applications/science/logic/eprover/default.nix
+++ b/pkgs/applications/science/logic/eprover/default.nix
@@ -20,7 +20,11 @@ stdenv.mkDerivation {
 
   buildInputs = [ which ];
 
-  preConfigure = "sed -e 's@^EXECPATH\\s.*@EXECPATH = '\$out'/bin@' -i Makefile.vars";
+  preConfigure = ''
+    sed -e 's@^EXECPATH\\s.*@EXECPATH = '\$out'/bin@' \
+    -e 's/^CC *= gcc$//' \
+    -i Makefile.vars
+  '';
 
   buildPhase = "make install";
 
@@ -34,6 +38,8 @@ stdenv.mkDerivation {
   meta = {
     inherit (s) version;
     description = "Automated theorem prover for full first-order logic with equality";
+    homepage = http://www.eprover.org/;
+    license = stdenv.lib.licenses.gpl2;
     maintainers = [stdenv.lib.maintainers.raskin];
     platforms = stdenv.lib.platforms.all;
   };
diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix
index 98b71b7f5007e..6c51fb5192d4d 100644
--- a/pkgs/applications/science/logic/isabelle/default.nix
+++ b/pkgs/applications/science/logic/isabelle/default.nix
@@ -1,23 +1,23 @@
-{ stdenv, fetchurl, perl, nettools, java, polyml, proofgeneral }:
+{ stdenv, fetchurl, perl, nettools, java, polyml }:
 # nettools needed for hostname
 
 let
-  dirname = "Isabelle2015";
+  dirname = "Isabelle2016";
   theories = ["HOL" "FOL" "ZF"];
 in
 
 stdenv.mkDerivation {
-  name = "isabelle-2015";
+  name = "isabelle-2016";
   inherit dirname theories;
 
   src = if stdenv.isDarwin
     then fetchurl {
-      url = http://isabelle.in.tum.de/dist/Isabelle2015.dmg;
-      sha256 = "1vhm10qc1rn3wy9r12clrl33p64h3q1aj41mcnxkbnsyg2bx03im";
+      url = "http://isabelle.in.tum.de/website-${dirname}/dist/${dirname}.dmg";
+      sha256 = "0wawf0cjc52h8hif1867p33qhlh6qz0fy5i2kr1gbf7psickd6iw";
     }
     else fetchurl {
-      url = http://isabelle.in.tum.de/dist/Isabelle2015_linux.tar.gz;
-      sha256 = "13kqm458d8mw7il1zg5bdb1nfbb869p331d75xzlm2v9xgjxx862";
+      url = "http://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_linux.tar.gz";
+      sha256 = "0jh1qrsyib13fycymwvw7dq7xfy4iyplwq0s65ash842cdzkbxb4";
     };
 
   buildInputs = [ perl polyml ]
@@ -34,17 +34,14 @@ stdenv.mkDerivation {
       --replace /usr/bin/env $ENV
     sed -i 's|isabelle_java java|${java}/bin/java|g' lib/Tools/java
     substituteInPlace etc/settings \
-      --subst-var-by ML_HOME "${polyml}/bin" \
-      --subst-var-by PROOFGENERAL_HOME "${proofgeneral}/share/emacs/site-lisp/ProofGeneral"
+      --subst-var-by ML_HOME "${polyml}/bin"
     substituteInPlace contrib/jdk/etc/settings \
       --replace ISABELLE_JDK_HOME= '#ISABELLE_JDK_HOME='
     substituteInPlace contrib/polyml-*/etc/settings \
-      --replace 'ML_HOME="$POLYML_HOME/$ML_PLATFORM"' \
-                "ML_HOME=\"${polyml}/bin\""
-  '';
-
-  buildPhase = ''
-    ISABELLE_JDK_HOME=${java} ./bin/isabelle build -s $theories
+      --replace '$POLYML_HOME/$ML_PLATFORM' ${polyml}/bin \
+      --replace '$POLYML_HOME/$PLATFORM/polyml' ${polyml}/bin/poly
+    substituteInPlace lib/scripts/run-polyml* lib/scripts/polyml-version \
+      --replace '$ML_HOME/poly' ${polyml}/bin/poly
   '';
 
   installPhase = ''
diff --git a/pkgs/applications/science/logic/ltl2ba/default.nix b/pkgs/applications/science/logic/ltl2ba/default.nix
index cdadd18ac9f52..f9bdd9a6b3b9f 100644
--- a/pkgs/applications/science/logic/ltl2ba/default.nix
+++ b/pkgs/applications/science/logic/ltl2ba/default.nix
@@ -9,6 +9,11 @@ stdenv.mkDerivation rec {
     sha256 = "16z0gc7a9dkarwn0l6rvg5jdhw1q4qyn4501zlchy0zxqddz0sx6";
   };
 
+  preConfigure = ''
+    substituteInPlace Makefile \
+    --replace "CC=gcc" ""
+  '';
+
   installPhase = ''
     mkdir -p $out/bin
     mv ltl2ba $out/bin
@@ -18,7 +23,7 @@ stdenv.mkDerivation rec {
     description = "fast translation from LTL formulae to Buchi automata";
     homepage    = "http://www.lsv.ens-cachan.fr/~gastin/ltl2ba";
     license     = stdenv.lib.licenses.gpl2Plus;
-    platforms   = stdenv.lib.platforms.linux;
+    platforms   = stdenv.lib.platforms.darwin ++ stdenv.lib.platforms.linux;
     maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
   };
 }
diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix
index 0313467ed7896..0eb51ff1620bb 100644
--- a/pkgs/applications/science/logic/why3/default.nix
+++ b/pkgs/applications/science/logic/why3/default.nix
@@ -2,15 +2,20 @@
 
 stdenv.mkDerivation rec {
   name    = "why3-${version}";
-  version = "0.86.2";
+  version = "0.86.3";
 
   src = fetchurl {
-    url    = https://gforge.inria.fr/frs/download.php/file/35214/why3-0.86.2.tar.gz;
-    sha256 = "08sa7dmp6yp29xn0m6h98nic4q47vb4ahvaid5drwh522pvwvg10";
+    url    = https://gforge.inria.fr/frs/download.php/file/35537/why3-0.86.3.tar.gz;
+    sha256 = "0sph6i4ga9450bk60wpm5cq3psw3g8xprnac7yjfq64iqz1dyz03";
   };
 
-  buildInputs = with ocamlPackages;
-    [ coq coq.camlp5 ocaml findlib lablgtk ocamlgraph zarith menhir ];
+  buildInputs = (with ocamlPackages; [
+      ocaml findlib lablgtk ocamlgraph zarith menhir ]) ++
+    stdenv.lib.optionals (ocamlPackages.ocaml == coq.ocaml ) [
+      coq coq.camlp5
+    ];
+
+  installTargets = [ "install" "install-lib" ];
 
   meta = with stdenv.lib; {
     description = "A platform for deductive program verification";
diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix
new file mode 100644
index 0000000000000..8673d7debd9de
--- /dev/null
+++ b/pkgs/applications/science/math/calc/default.nix
@@ -0,0 +1,45 @@
+{ stdenv, fetchurl, makeWrapper, glibc, readline, ncurses, groff, utillinux }:
+
+with stdenv.lib;
+let
+  makeFlags = ''
+    INCDIR=${glibc}/include \
+    BINDIR=$out/bin LIBDIR=$out/lib CALC_INCDIR=$out/include/calc CALC_SHAREDIR=$out/share/calc MANDIR=$out/share/man/man1 \
+    USE_READLINE=-DUSE_READLINE READLINE_LIB=-lreadline READLINE_EXTRAS='-lhistory -lncurses' \
+    TERMCONTROL=-DUSE_TERMIOS \
+    NROFF=groff
+  '';
+in
+stdenv.mkDerivation rec {
+
+  name = "calc-${version}";
+  version = "2.12.5.3";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/calc/${name}.tar.bz2";
+    sha256 = "14mnz6smhi3a0rgmwvddk9w3vdisi8khq67i8nqsl47vgs8n1kqg";
+  };
+
+  buildInputs = [ makeWrapper readline ncurses groff utillinux ];
+
+  configurePhase = ''
+    sed -i 's/all: check_include/all:/' Makefile
+  '';
+
+  buildPhase = ''
+    make ${makeFlags}
+  '';
+
+  installPhase = ''
+    make install ${makeFlags}
+    wrapProgram $out/bin/calc --prefix LD_LIBRARY_PATH : $out/lib
+  '';
+
+  meta = {
+    description = "C-style arbitrary precision calculator";
+    homepage = http://www.isthe.com/chongo/tech/comp/calc/;
+    license = licenses.lgpl21;
+    maintainers = [ ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/applications/science/math/lp_solve/default.nix b/pkgs/applications/science/math/lp_solve/default.nix
index 09af2d708c965..7726793fcaf83 100644
--- a/pkgs/applications/science/math/lp_solve/default.nix
+++ b/pkgs/applications/science/math/lp_solve/default.nix
@@ -32,7 +32,7 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    description = "lp_solve is a Mixed Integer Linear Programming (MILP) solver.";
+    description = "lp_solve is a Mixed Integer Linear Programming (MILP) solver";
     homepage    = "http://lpsolve.sourceforge.net";
     license     = licenses.gpl2Plus;
     maintainers = with maintainers; [ smironov ];
diff --git a/pkgs/applications/science/misc/motu-client/default.nix b/pkgs/applications/science/misc/motu-client/default.nix
new file mode 100644
index 0000000000000..b5e9fa6a51ee8
--- /dev/null
+++ b/pkgs/applications/science/misc/motu-client/default.nix
@@ -0,0 +1,23 @@
+{ python27Packages, fetchurl, lib } :
+python27Packages.buildPythonApplication rec {
+  name = "motu-client-${version}";
+  version = "1.0.8";
+
+  src = fetchurl {
+    url = "https://github.com/quiet-oceans/motuclient-setuptools/archive/${name}.tar.gz";
+    sha256 = "1naqmav312agn72iad9kyxwscn2lz4v1cfcqqi1qcgvc82vnwkw2";
+  };
+
+  meta = with lib; {
+    homepage = https://github.com/quiet-oceans/motuclient-setuptools;
+    description = "CLI to query oceanographic data to Motu servers";
+    longDescription = ''
+      Access data from (motu)[http://sourceforge.net/projects/cls-motu/] servers.
+      This is a refactored fork of the original release in order to simplify integration,
+      deployment and packaging. Upstream code can be found at
+      http://sourceforge.net/projects/cls-motu/ .
+    '';
+    license = licenses.lgpl3Plus;
+    maintainers = [ maintainers.lsix ];
+  };
+}
diff --git a/pkgs/applications/science/misc/yarp/default.nix b/pkgs/applications/science/misc/yarp/default.nix
new file mode 100644
index 0000000000000..2daf5a4b5c7d4
--- /dev/null
+++ b/pkgs/applications/science/misc/yarp/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub, pkgconfig, cmake, ace
+}:
+
+stdenv.mkDerivation rec {
+  name = "yarp-${version}";
+  version = "2.3.64";
+  src = fetchFromGitHub {
+    owner = "robotology";
+    repo = "yarp";
+    rev = "v2.3.64";
+    sha256 = "0x9sdc8d6rppzf1kx53w0yjlnmz7h75qv62yd3ls09w3cy7nb5x7";
+  };
+
+  buildInputs = [ cmake ace ];
+
+  enableParallelBuilding = true;
+
+  meta = {
+    description = "Yet Another Robot Platform";
+    homepage = http://yarp.it;
+    license = stdenv.lib.licenses.lgpl21;
+    platforms = stdenv.lib.platforms.linux;
+    maintainers = [ stdenv.lib.maintainers.nico202 ];
+  };
+}
+
diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
index 43ef4337d5730..5724db9f3069b 100644
--- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
@@ -1,22 +1,30 @@
 
 { stdenv, fetchurl, cmake,
   singlePrec ? true,
-  fftw
+  mpiEnabled ? false,
+  fftw,
+  openmpi
 }:
 
 
 stdenv.mkDerivation {
-  name = "gromacs-4.6.5";
+  name = "gromacs-4.6.7";
 
   src = fetchurl {
-    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz";
-    sha256 = "02ggrplh8fppqib86y3rfk4qm08yddlrb1yjgzl138b3b4qjy957";
+    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz";
+    sha256 = "6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9";
   };
 
-  buildInputs = [cmake fftw];
+  buildInputs = [cmake fftw]
+  ++ (stdenv.lib.optionals mpiEnabled [ openmpi ]);
 
   cmakeFlags = ''
     ${if singlePrec then "-DGMX_DOUBLE=OFF" else "-DGMX_DOUBLE=ON -DGMX_DEFAULT_SUFFIX=OFF"}
+    ${if mpiEnabled then "-DGMX_MPI:BOOL=TRUE 
+                          -DGMX_CPU_ACCELERATION:STRING=SSE4.1 
+                          -DGMX_OPENMP:BOOL=TRUE
+                          -DGMX_THREAD_MPI:BOOL=FALSE"
+                     else "-DGMX_MPI:BOOL=FALSE" }
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/science/spyder/default.nix b/pkgs/applications/science/spyder/default.nix
index 9e74a23323653..73847624e85a6 100644
--- a/pkgs/applications/science/spyder/default.nix
+++ b/pkgs/applications/science/spyder/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, unzip, buildPythonPackage, makeDesktopItem
+{ stdenv, fetchurl, unzip, buildPythonApplication, makeDesktopItem
 # mandatory
 , pyside
 # recommended
@@ -7,7 +7,7 @@
 , ipython ? null, pylint ? null, pep8 ? null
 }:
 
-buildPythonPackage rec {
+buildPythonApplication rec {
   name = "spyder-${version}";
   version = "2.3.8";
   namePrefix = "";