Merge branch 'staging'

pkgs/development/compilers/llvm/3.9/clang/default.nix

@@ -6,7 +6,7 @@ let
     name = "clang-${version}";
 
     unpackPhase = ''
-      unpackFile ${fetch "cfe" "0a1x32rxrq4ln079xf58irg56gjdxcfgwa00ws4hqv9pv73sg5km"}
+      unpackFile ${fetch "cfe" "0qsyyb40iwifhhlx9a3drf8z6ni6zwyk3bvh0kx2gs6yjsxwxi76"}
       mv cfe-${version}.src clang
       sourceRoot=$PWD/clang
       unpackFile ${clang-tools-extra_src}

pkgs/development/compilers/llvm/3.9/default.nix

@@ -2,7 +2,7 @@
 let
   callPackage = newScope (self // { inherit stdenv isl version fetch; });
 
-  version = "3.9.0";
+  version = "3.9.1";
 
   fetch = fetch_v version;
   fetch_v = ver: name: sha256: fetchurl {
@@ -10,8 +10,8 @@ let
     inherit sha256;
   };
 
-  compiler-rt_src = fetch "compiler-rt" "16m5g0hf8yg9npnw25j2a86g34nsvk9rsm3c84gbch2prm7j5rg0";
+  compiler-rt_src = fetch "compiler-rt" "16gc2gdmp5c800qvydrdhsp0bzb97s8wrakl6i8a4lgslnqnf2fk";
-  clang-tools-extra_src = fetch "clang-tools-extra" "052zg0h5vbmxnh2ikc743rw3649f112dfyn8hg39x6cfxi3fqyjv";
+  clang-tools-extra_src = fetch "clang-tools-extra" "0d9nh7j7brbh9avigcn69dlaihsl9p3cf9s45mw6fxzzvrdvd999";
 
   self = {
     llvm = callPackage ./llvm.nix {

pkgs/development/compilers/llvm/3.9/libc++/default.nix

@@ -3,7 +3,7 @@
 stdenv.mkDerivation rec {
   name = "libc++-${version}";
 
-  src = fetch "libcxx" "01jvgwi9zd46bb1f93c561212bjzg02q2akacvsj4qsw6r8qvcyh";
+  src = fetch "libcxx" "0qbl3afl2p2h87p977lsqr5kykl6cgjpkzczs0g6a3pn53j1bri5";
 
   postUnpack = ''
     unpackFile ${libcxxabi.src}

pkgs/development/compilers/llvm/3.9/libc++abi.nix

@@ -3,7 +3,7 @@
 stdenv.mkDerivation {
   name = "libc++abi-${version}";
 
-  src = fetch "libcxxabi" "06c05jlwfgm2q5xhy5wzmsi9bmfphzh22wpmbph84s452wksjdxh";
+  src = fetch "libcxxabi" "1qi9q06zanqm8awzq83810avmvi52air6gr9zfip8mbg5viqn3cj";
 
   buildInputs = [ cmake ] ++ stdenv.lib.optional (!stdenv.isDarwin && !stdenv.isFreeBSD) libunwind;
 

pkgs/development/compilers/llvm/3.9/lldb.nix

@@ -15,7 +15,7 @@
 stdenv.mkDerivation {
   name = "lldb-${version}";
 
-  src = fetch "lldb" "1113s6crh94hzk9h9lqrvng0lsy174ml2rq0r962ngqy843hwa31";
+  src = fetch "lldb" "1z30ljmcpp261bjng1i5k3bb9jkrs1cr97z04qs4s3zql6r12cvy";
 
   postUnpack = ''
     # Hack around broken standalone build as of 3.8

pkgs/development/compilers/llvm/3.9/llvm.nix

@@ -19,7 +19,7 @@
 }:
 
 let
-  src = fetch "llvm" "0j49lkd5d7nnpdqzaybs2472bvcxyx0i4r3iccwf3kj2v9wk3iv6";
+  src = fetch "llvm" "1vi9sf7rx1q04wj479rsvxayb6z740iaz3qniwp266fgp5a07n8z";
   shlib = if stdenv.isDarwin then "dylib" else "so";
 
   # Used when creating a version-suffixed symlink of libLLVM.dylib

pkgs/development/libraries/libssh2/default.nix

@@ -1,11 +1,11 @@
 {stdenv, fetchurlBoot, openssl, zlib, windows}:
 
 stdenv.mkDerivation rec {
-  name = "libssh2-1.7.0";
+  name = "libssh2-1.8.0";
 
   src = fetchurlBoot {
     url = "${meta.homepage}/download/${name}.tar.gz";
-    sha256 = "116mh112w48vv9k3f15ggp5kxw5sj4b88dzb5j69llsh7ba1ymp4";
+    sha256 = "1m3n8spv79qhjq4yi0wgly5s5rc8783jb1pyra9bkx1md0plxwrr";
   };
 
   outputs = [ "out" "dev" "devdoc" ];

pkgs/development/libraries/ncurses/default.nix

@@ -91,6 +91,12 @@ stdenv.mkDerivation rec {
           if [ -e "$out/lib/lib''${library}$suffix.$dylibtype" ]; then
             ln -svf lib''${library}$suffix.$dylibtype $out/lib/lib$library$newsuffix.$dylibtype
             ln -svf lib''${library}$suffix.$dylibtype.${abiVersion} $out/lib/lib$library$newsuffix.$dylibtype.${abiVersion}
+            if [ "ncurses" = "$library" ]
+            then
+              # make libtinfo symlinks
+              ln -svf lib''${library}$suffix.$dylibtype $out/lib/libtinfo$newsuffix.$dylibtype
+              ln -svf lib''${library}$suffix.$dylibtype.${abiVersion} $out/lib/libtinfo$newsuffix.$dylibtype.${abiVersion}
+            fi
           fi
         done
         for statictype in a dll.a la; do
@@ -102,9 +108,6 @@ stdenv.mkDerivation rec {
       done
     done
 
-    # create libtinfo symlink
-    ln -svf $out/lib/libncurses.$dylibtype $out/libtinfo.$dylibtype
-        
     # move some utilities to $bin
     # these programs are used at runtime and don't really belong in $dev
     moveToOutput "bin/clear" "$out"

pkgs/development/python-modules/numpy.nix

@@ -39,15 +39,18 @@ in buildPythonPackage (args // rec {
     runHook postCheck
   '';
 
+  postInstall = ''
+    ln -s $out/bin/f2py* $out/bin/f2py
+  '';
+
   passthru = {
     blas = blas;
   };
 
-  # The large file support test is disabled because it takes forever
+  # Disable two tests
-  # and can cause the machine to run out of disk space when run.
+  # - test_f2py: f2py isn't yet on path.
-  prePatch = ''
+  # - test_large_file_support: takes a long time and can cause the machine to run out of disk space
-    sed -i 's/test_large_file_support/donttest/' numpy/lib/tests/test_format.py
+  NOSE_EXCLUDE="test_f2py,test_large_file_support";
-  '';
 
   meta = {
     description = "Scientific tools for Python";

pkgs/top-level/python-packages.nix

@@ -16142,10 +16142,10 @@ in {
   };
 
   numpy_1_11 = self.buildNumpyPackage rec {
-    version = "1.11.2";
+    version = "1.11.3";
     src = pkgs.fetchurl {
-      url = "mirror://pypi/n/numpy/numpy-${version}.tar.gz";
+      url = "mirror://pypi/n/numpy/numpy-${version}.zip";
-      sha256 = "04db2fbd64e2e7c68e740b14402b25af51418fc43a59d9e54172b38b906b0f69";
+      sha256 = "2e0fc5248246a64628656fe14fcab0a959741a2820e003bd15538226501b82f7";
     };
   };
 
@@ -24466,12 +24466,8 @@ in {
     LC_ALL = "en_US.UTF-8";
     buildInputs = with self; [ nose simplejson mock pkgs.glibcLocales html5lib ] ++ optional (pythonOlder "3.4") self.enum34;
     # Disable two tests that require network access.
-    postPatch = ''
-      substituteInPlace tests/test_build_linkcheck.py --replace test_defaults dont_test_defaults
-      substituteInPlace tests/test_build_linkcheck.py --replace test_anchors_ignored dont_test_anchors_ignored
-    '';
     checkPhase = ''
-      make test
+      NOSE_EXCLUDE=test_defaults,test_anchors_ignored make test
     '';
     propagatedBuildInputs = with self; [
       docutils