Merge remote-tracking branch 'upstream/master' into HEAD

3 files changed, 71 insertions, 86 deletions

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 9511dde16c8a..211bd1f70f10 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -105,6 +105,8 @@ with pkgs;
 
   docker_compose = pythonPackages.docker_compose;
 
+  dotfiles = callPackage ../applications/misc/dotfiles { };
+
   dotnetenv = callPackage ../build-support/dotnetenv {
     dotnetfx = dotnetfx40;
   };
@@ -789,7 +791,9 @@ with pkgs;
 
   burpsuite = callPackage ../tools/networking/burpsuite {};
 
-  c3d = callPackage ../applications/graphics/c3d {};
+  c3d = callPackage ../applications/graphics/c3d {
+    inherit (darwin.apple_sdk.frameworks) Cocoa;
+  };
 
   cabal2nix = haskell.lib.overrideCabal haskellPackages.cabal2nix (drv: {
     isLibrary = false;
@@ -1294,7 +1298,9 @@ with pkgs;
 
   atool = callPackage ../tools/archivers/atool { };
 
-  bsc = callPackage ../tools/compression/bsc { };
+  bsc = callPackage ../tools/compression/bsc {
+    inherit (llvmPackages) openmp;
+  };
 
   bzip2 = callPackage ../tools/compression/bzip2 { };
 
@@ -1451,7 +1457,7 @@ with pkgs;
       clangStdenv = libcxxStdenv; # workaround for https://github.com/NixOS/nixpkgs/issues/28223
       python = python2;
       inherit (python2Packages) gyp;
-      protobuf = protobuf3_2.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
+      protobuf = pkgs.protobuf.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
     };
 
     table = callPackage ../tools/inputmethods/ibus-engines/ibus-table {
@@ -1938,7 +1944,7 @@ with pkgs;
       clangStdenv = libcxxStdenv; # workaround for https://github.com/NixOS/nixpkgs/issues/28223
       python = python2;
       inherit (python2Packages) gyp;
-      protobuf = protobuf3_2.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
+      protobuf = pkgs.protobuf.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
     };
 
     table-other = callPackage ../tools/inputmethods/fcitx-engines/fcitx-table-other { };
@@ -2797,6 +2803,10 @@ with pkgs;
 
   kpcli = callPackage ../tools/security/kpcli { };
 
+  # kget is part of kde-applications but the released version is still for KDE 4
+  # This needs to move to the proper place when the "frameworks" branch is released
+  kget = libsForQt5.callPackage ../applications/networking/kget { };
+
   krename = libsForQt5.callPackage ../applications/misc/krename { };
 
   kronometer = libsForQt5.callPackage ../tools/misc/kronometer { };
@@ -5229,9 +5239,7 @@ with pkgs;
     stdenv = overrideCC stdenv gcc49;
   };
 
-  bigloo = callPackage ../development/compilers/bigloo {
-    stdenv = overrideCC stdenv gcc49;
-  };
+  bigloo = callPackage ../development/compilers/bigloo { };
 
   binaryen = callPackage ../development/compilers/binaryen { };
 
@@ -5500,7 +5508,7 @@ with pkgs;
     isl = isl_0_17;
   }));
 
-  gfortran = gfortran5;
+  gfortran = gfortran6;
 
   gfortran48 = wrapCC (gcc48.cc.override {
     name = "gfortran";
@@ -6354,7 +6362,7 @@ with pkgs;
   mesos = callPackage ../applications/networking/cluster/mesos {
     sasl = cyrus_sasl;
     inherit (pythonPackages) python boto setuptools wrapPython;
-    pythonProtobuf = pythonPackages.protobuf2_6;
+    pythonProtobuf = pythonPackages.protobuf;
     perf = linuxPackages.perf;
   };
 
@@ -7547,6 +7555,8 @@ with pkgs;
 
   afflib = callPackage ../development/libraries/afflib { };
 
+  aften = callPackage ../development/libraries/aften { };
+
   alure = callPackage ../development/libraries/alure { };
 
   agg = callPackage ../development/libraries/agg { };
@@ -9988,17 +9998,11 @@ with pkgs;
 
   postgis = callPackage ../development/libraries/postgis { };
 
-  protobuf = protobuf2_6;
-  protobuf3_0 = lowPrio (callPackage ../development/libraries/protobuf/3.0.nix { });
+  protobuf = callPackage ../development/libraries/protobuf/3.4.nix { };
+
   protobuf3_1 = callPackage ../development/libraries/protobuf/3.1.nix { };
-  protobuf3_2 = callPackage ../development/libraries/protobuf/3.2.nix { };
-  protobuf3_3 = callPackage ../development/libraries/protobuf/3.3.nix { };
-  protobuf2_6 = callPackage ../development/libraries/protobuf/2.6.nix { };
-  protobuf2_5 = callPackage ../development/libraries/protobuf/2.5.nix { };
 
-  protobufc = protobufc1_1;
-  protobufc1_1 = callPackage ../development/libraries/protobufc/1.1.nix { };
-  protobufc1_0 = callPackage ../development/libraries/protobufc/1.0.nix { };
+  protobufc = callPackage ../development/libraries/protobufc/1.3.nix { };
 
   flatbuffers = callPackage ../development/libraries/flatbuffers { };
 
@@ -16070,7 +16074,7 @@ with pkgs;
   seafile-client = libsForQt5.callPackage ../applications/networking/seafile-client { };
 
   seeks = callPackage ../tools/networking/p2p/seeks {
-    protobuf = protobuf2_5;
+    protobuf = protobuf3_1;
   };
 
   seg3d = callPackage ../applications/graphics/seg3d {
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index 475d456eb237..a8282ba6f6bb 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -5159,10 +5159,10 @@ let self = _self // overrides; _self = with self; {
   };
 
   ExtUtilsParseXS = buildPerlPackage rec {
-    name = "ExtUtils-ParseXS-3.24";
+    name = "ExtUtils-ParseXS-3.35";
     src = fetchurl {
       url = "mirror://cpan/authors/id/S/SM/SMUELLER/${name}.tar.gz";
-      sha256 = "07ipa2ssflw3ais8gbjdk4l8z2k1p65nfjwkxm37g6zw1210pdih";
+      sha256 = "077fqiyabydm8j34wxzxwxskyidh8nmwq9gskaxai8kq298z1pj1";
     };
   };
 
@@ -5218,10 +5218,10 @@ let self = _self // overrides; _self = with self; {
   };
 
   ExtUtilsXSpp = buildPerlModule rec {
-    name = "ExtUtils-XSpp-0.1700";
+    name = "ExtUtils-XSpp-0.18";
     src = fetchurl {
       url = "mirror://cpan/modules/by-module/ExtUtils/${name}.tar.gz";
-      sha256 = "1msp79bdjzi59vignfz1cxwk5a2cjiahblvi0ka60pi8nnn0alrm";
+      sha256 = "1zx84f93lkymqz7qa4d63gzlnhnkxm5i3gvsrwkvvqr9cxjasxli";
     };
     buildInputs = [ Spiffy TestBase TestDifferences ];
   };
@@ -5528,11 +5528,16 @@ let self = _self // overrides; _self = with self; {
     };
   };
 
-  FileModified = buildPerlPackage {
-    name = "File-Modified-0.07";
+  FileModified = buildPerlPackage rec {
+    name = "File-Modified-0.10";
     src = fetchurl {
-      url = mirror://cpan/authors/id/C/CO/CORION/File-Modified-0.07.tar.gz;
-      sha256 = "11zkg171fa5vdbyrbfcay134hhgyf4yaincjxwspwznrfmkpi49h";
+      url = "mirror://cpan/authors/id/N/NE/NEILB/${name}.tar.gz";
+      sha256 = "6b50b1aab6ec6998a017f6403c2735b3bc1e1cf46187bd134d7eb6df3fc45144";
+    };
+    meta = {
+      homepage = https://github.com/neilbowers/File-Modified;
+      description = "Checks intelligently if files have changed";
+      license = with stdenv.lib.licenses; [ artistic1 gpl1Plus ];
     };
   };
 
@@ -5755,10 +5760,10 @@ let self = _self // overrides; _self = with self; {
   };
 
   FilterSimple = buildPerlPackage {
-    name = "Filter-Simple-0.91";
+    name = "Filter-Simple-0.94";
     src = fetchurl {
-      url = mirror://cpan/authors/id/S/SM/SMUELLER/Filter-Simple-0.91.tar.gz;
-      sha256 = "c75a4945e94ecfe97e1409f49df036700d2e072e288497e205c4d319a80f694d";
+      url = mirror://cpan/authors/id/S/SM/SMUELLER/Filter-Simple-0.94.tar.gz;
+      sha256 = "1lkrgsqaxf595ha1y29gxqqf4kf8cpm5yzr4gg7zngbq1nb0pz6g";
     };
     meta = {
       description = "Simplified source filtering";
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index aebb8e2be771..abd2de9ae405 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -227,9 +227,7 @@ in {
 
   pycryptodomex = callPackage ../development/python-modules/pycryptodomex { };
 
-  PyChromecast = callPackage ../development/python-modules/pychromecast {
-    protobuf = self.protobuf3_2;
-  };
+  PyChromecast = callPackage ../development/python-modules/pychromecast { };
 
   pyexiv2 = if (!isPy3k) then callPackage ../development/python-modules/pyexiv2 {} else throw "pyexiv2 not supported for interpreter ${python.executable}";
 
@@ -261,7 +259,7 @@ in {
     pythonPackages = self;
   };
 
-  pyscard = callPackage ../development/python-modules/pyscard { };
+  pyscard = callPackage ../development/python-modules/pyscard { inherit (pkgs.darwin.apple_sdk.frameworks) PCSC; };
 
   pyside = callPackage ../development/python-modules/pyside { };
 
@@ -4528,6 +4526,8 @@ in {
 
   libtmux = callPackage ../development/python-modules/libtmux { };
 
+  linuxfd = callPackage ../development/python-modules/linuxfd { };
+
   locket = buildPythonPackage rec {
     name = "locket-${version}";
     version = "0.2.0";
@@ -5119,23 +5119,6 @@ in {
     };
   };
 
-  dotfiles = buildPythonPackage rec {
-    name = "dotfiles-0.6.3";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/d/dotfiles/${name}.tar.gz";
-      sha256 = "45ecfd7f2ed9d0f2a7ac632c9bd0ebdca758d8bbc2b6f11562579d525f0467b8";
-    };
-
-    doCheck = true;
-
-    meta = {
-      description = "Easily manage your dotfiles";
-      homepage = https://github.com/jbernard/dotfiles;
-      license = licenses.isc;
-    };
-  };
-
   dopy = buildPythonPackage rec {
     version = "2016-01-04";
     name = "dopy-${version}";
@@ -5916,7 +5899,7 @@ in {
       validictory
       decorator
       mutagen
-      protobuf3_0
+      protobuf
       setuptools
       requests
       dateutil
@@ -7536,7 +7519,7 @@ in {
       sha256 = "09bf5gfip9x2wr0ij43p39ac6z2iqzn7kgpi2jjbwpnhs0vwkycs";
     };
 
-    propagatedBuildInputs = with self; [ python-axolotl-curve25519 protobuf3_0 pycrypto ];
+    propagatedBuildInputs = with self; [ python-axolotl-curve25519 protobuf pycrypto ];
     # IV == 0 in tests is not supported by pycrytpodom (our pycrypto drop-in)
     doCheck = !isPy3k;
 
@@ -10099,14 +10082,14 @@ in {
 
   glances = buildPythonPackage rec {
     name = "glances-${version}";
-    version = "2.11";
+    version = "2.11.1";
     disabled = isPyPy;
 
     src = pkgs.fetchFromGitHub {
       owner = "nicolargo";
       repo = "glances";
       rev = "v${version}";
-      sha256 = "01vnrr37jbpzrz6w670l3g3bv60xl50w41rn1dl99wp2fr460ndn";
+      sha256 = "1n3x0bkydlqmxdr0wdgfgichp8fyldzkaijj618y5ns2k5qiwsxr";
     };
 
     doCheck = false;
@@ -10122,7 +10105,7 @@ in {
       homepage = "https://nicolargo.github.io/glances/";
       description = "Cross-platform curses-based monitoring tool";
       license = licenses.lgpl3;
-      maintainers = with maintainers; [ koral ];
+      maintainers = with maintainers; [ primeos koral ];
     };
   };
 
@@ -15031,7 +15014,7 @@ in {
     };
 
     propagatedBuildInputs = with self; [
-      pbr argparse six webob
+      pbr six webob
     ];
     buildInputs = with self; [
       oslosphinx coverage mock subunit testrepository testtools
@@ -15039,6 +15022,7 @@ in {
 
     patchPhase = ''
       sed -i 's@python@${python.interpreter}@' .testr.conf
+      substituteInPlace requirements.txt --replace "argparse" ""
     '';
   };
 
@@ -16342,30 +16326,16 @@ in {
 
   });
 
-  protobuf = self.protobuf2_6;
-  protobuf3_3 = callPackage ../development/python-modules/protobuf.nix {
-    disabled = isPyPy;
-    doCheck = !isPy3k;
-    protobuf = pkgs.protobuf3_3;
-  };
-  protobuf3_2 = callPackage ../development/python-modules/protobuf.nix {
+  protobuf = callPackage ../development/python-modules/protobuf.nix {
     disabled = isPyPy;
     doCheck = !isPy3k;
-    protobuf = pkgs.protobuf3_2;
+    protobuf = pkgs.protobuf;
   };
-  protobuf3_0 = callPackage ../development/python-modules/protobuf.nix {
+
+  protobuf3_1 = callPackage ../development/python-modules/protobuf.nix {
     disabled = isPyPy;
     doCheck = !isPy3k;
-    protobuf = pkgs.protobuf3_0;
-  };
-  protobuf2_6 = callPackage ../development/python-modules/protobuf.nix {
-    disabled = isPy3k || isPyPy;
-    doCheck = false;
-    protobuf = pkgs.protobuf2_6;
-  };
-  protobuf2_5 = callPackage ../development/python-modules/protobuf.nix {
-    disabled = isPy3k || isPyPy;
-    protobuf = pkgs.protobuf2_5;
+    protobuf = pkgs.protobuf3_1;
   };
 
   psd-tools = callPackage ../development/python-modules/psd-tools { };
@@ -23891,9 +23861,7 @@ EOF
     inherit (pkgs) libasyncns pkgconfig;
   };
 
-  libarcus = callPackage ../development/python-modules/libarcus {
-    protobuf = self.protobuf3_0;
-  };
+  libarcus = callPackage ../development/python-modules/libarcus { };
 
   pybrowserid = buildPythonPackage rec {
     name = "PyBrowserID-${version}";
@@ -24175,7 +24143,7 @@ EOF
     '';
 
     buildInputs = with self; [ nose ];
-    propagatedBuildInputs = with self; [ noise numpy pyplatec protobuf3_2 purepng argparse h5py gdal ];
+    propagatedBuildInputs = with self; [ noise numpy pyplatec protobuf purepng argparse h5py gdal ];
 
     prePatch = ''
       substituteInPlace setup.py \
@@ -24267,11 +24235,15 @@ EOF
     };
 
     # Fix the USB backend library lookup
-    postPatch = ''
-      libusb=${pkgs.libusb1.out}/lib/libusb-1.0.so
-      test -f $libusb || { echo "ERROR: $libusb doesn't exist, please update/fix this build expression."; exit 1; }
-      sed -i -e "s|find_library=None|find_library=lambda _:\"$libusb\"|" usb/backend/libusb1.py
-    '';
+    postPatch =
+      let
+        # This should really be in the stdenv somewhere
+        soext = if stdenv.isLinux then "so" else if stdenv.isDarwin then "dylib" else throw "Unsupported platform";
+      in ''
+        libusb=${pkgs.libusb1.out}/lib/libusb-1.0.${soext}
+        test -f $libusb || { echo "ERROR: $libusb doesn't exist, please update/fix this build expression."; exit 1; }
+        sed -i -e "s|find_library=None|find_library=lambda _:\"$libusb\"|" usb/backend/libusb1.py
+      '';
 
     propagatedBuildInputs = [ pkgs.libusb ];
 
@@ -25422,10 +25394,14 @@ EOF
       sha256 = "99ab03bffdb30d9ec98724898f428f8e73129483417d5892799a0f0d2249f233";
     };
 
+    patchPhase = ''
+      substituteInPlace setup.py --replace '"argparse",' ""
+    '';
+
     # ImportError: No module named tests
     doCheck = false;
 
-    propagatedBuildInputs = with self; [ ofxhome ofxparse beautifulsoup keyring argparse ];
+    propagatedBuildInputs = with self; [ ofxhome ofxparse beautifulsoup keyring ];
   };
 
   ofxhome = buildPythonPackage rec {