Merge branch 'master' into staging

maintainers/maintainer-list.nix

@@ -1929,6 +1929,11 @@
     github = "kaiha";
     name = "Kai Harries";
   };
+  kalbasit = {
+    email = "wael.nasreddine@gmail.com";
+    github = "kalbasit";
+    name = "Wael Nasreddine";
+  };
   kamilchm = {
     email = "kamil.chm@gmail.com";
     github = "kamilchm";

nixos/doc/manual/release-notes/rl-1809.xml

@@ -18,6 +18,27 @@
   </para>
 
   <itemizedlist>
+   <listitem>
+     <para>
+       Support for wrapping binaries using <literal>firejail</literal> has been
+       added through <varname>programs.firejail.wrappedBinaries</varname>.
+     </para>
+     <para>
+       For example
+     </para>
+<programlisting>
+programs.firejail = {
+  enable = true;
+  wrappedBinaries = {
+    firefox = "${lib.getBin pkgs.firefox}/bin/firefox";
+    mpv = "${lib.getBin pkgs.mpv}/bin/mpv";
+  };
+};
+</programlisting>
+      <para>
+        This will place <literal>firefox</literal> and <literal>mpv</literal> binaries in the global path wrapped by firejail.
+      </para>
+   </listitem>
    <listitem>
     <para>
      User channels are now in the default <literal>NIX_PATH</literal>, allowing

nixos/modules/module-list.nix

@@ -86,6 +86,7 @@
   ./programs/dconf.nix
   ./programs/digitalbitbox/default.nix
   ./programs/environment.nix
+  ./programs/firejail.nix
   ./programs/fish.nix
   ./programs/freetds.nix
   ./programs/gnupg.nix

nixos/modules/programs/firejail.nix

@@ -0,0 +1,48 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+  cfg = config.programs.firejail;
+
+  wrappedBins = pkgs.stdenv.mkDerivation rec {
+    name = "firejail-wrapped-binaries";
+    nativeBuildInputs = with pkgs; [ makeWrapper ];
+    buildCommand = ''
+      mkdir -p $out/bin
+      ${lib.concatStringsSep "\n" (lib.mapAttrsToList (command: binary: ''
+      cat <<_EOF >$out/bin/${command}
+      #!${pkgs.stdenv.shell} -e
+      /run/wrappers/bin/firejail ${binary} "\$@"
+      _EOF
+      chmod 0755 $out/bin/${command}
+      '') cfg.wrappedBinaries)}
+    '';
+  };
+
+in {
+  options.programs.firejail = {
+    enable = mkEnableOption "firejail";
+
+    wrappedBinaries = mkOption {
+      type = types.attrs;
+      default = {};
+      description = ''
+        Wrap the binaries in firejail and place them in the global path.
+        </para>
+        <para>
+        You will get file collisions if you put the actual application binary in
+        the global environment and applications started via .desktop files are
+        not wrapped if they specify the absolute path to the binary.
+      '';
+    };
+  };
+
+  config = mkIf cfg.enable {
+    security.wrappers.firejail.source = "${lib.getBin pkgs.firejail}/bin/firejail";
+
+    environment.systemPackages = [ wrappedBins ];
+  };
+
+  meta.maintainers = with maintainers; [ peterhoeg ];
+}

nixos/modules/services/networking/ssh/sshd.nix

@@ -198,6 +198,10 @@ in
           [ { type = "rsa"; bits = 4096; path = "/etc/ssh/ssh_host_rsa_key"; }
             { type = "ed25519"; path = "/etc/ssh/ssh_host_ed25519_key"; }
           ];
+        example =
+          [ { type = "rsa"; bits = 4096; path = "/etc/ssh/ssh_host_rsa_key"; rounds = 100; openSSHFormat = true; }
+            { type = "ed25519"; path = "/etc/ssh/ssh_host_ed25519_key"; rounds = 100; comment = "key comment"; }
+          ];
         description = ''
           NixOS can automatically generate SSH host keys.  This option
           specifies the path, type and size of each key.  See
@@ -358,7 +362,14 @@ in
 
                 ${flip concatMapStrings cfg.hostKeys (k: ''
                   if ! [ -f "${k.path}" ]; then
-                      ssh-keygen -t "${k.type}" ${if k ? bits then "-b ${toString k.bits}" else ""} -f "${k.path}" -N ""
+                      ssh-keygen \
+                        -t "${k.type}" \
+                        ${if k ? bits then "-b ${toString k.bits}" else ""} \
+                        ${if k ? rounds then "-a ${toString k.rounds}" else ""} \
+                        ${if k ? comment then "-C '${k.comment}'" else ""} \
+                        ${if k ? openSSHFormat && k.openSSHFormat then "-o" else ""} \
+                        -f "${k.path}" \
+                        -N ""
                   fi
                 '')}
               '';
@@ -404,6 +415,9 @@ in
         unixAuth = cfg.passwordAuthentication;
       };
 
+    # These values are merged with the ones defined externally, see:
+    # https://github.com/NixOS/nixpkgs/pull/10155
+    # https://github.com/NixOS/nixpkgs/pull/41745
     services.openssh.authorizedKeysFiles =
       [ ".ssh/authorized_keys" ".ssh/authorized_keys2" "/etc/ssh/authorized_keys.d/%u" ];
 

nixos/modules/services/x11/desktop-managers/plasma5.nix

@@ -221,6 +221,11 @@ in
       security.pam.services.sddm.enableKwallet = true;
       security.pam.services.slim.enableKwallet = true;
 
+      # Update the start menu for each user that has `isNormalUser` set.
+      system.activationScripts.plasmaSetup = stringAfter [ "users" "groups" ]
+        (concatStringsSep "\n"
+          (mapAttrsToList (name: value: "${pkgs.su}/bin/su ${name} -c kbuildsycoca5")
+            (filterAttrs (n: v: v.isNormalUser) config.users.users)));
     })
   ];
 

nixos/modules/services/x11/display-managers/sddm.nix

@@ -19,17 +19,6 @@ let
 
   Xsetup = pkgs.writeScript "Xsetup" ''
     #!/bin/sh
-
-    # Prior to Qt 5.9.2, there is a QML cache invalidation bug which sometimes
-    # strikes new Plasma 5 releases. If the QML cache is not invalidated, SDDM
-    # will segfault without explanation. We really tore our hair out for awhile
-    # before finding the bug:
-    # https://bugreports.qt.io/browse/QTBUG-62302
-    # We work around the problem by deleting the QML cache before startup. It
-    # will be regenerated, causing a small but perceptible delay when SDDM
-    # starts.
-    rm -fr /var/lib/sddm/.cache/sddm-greeter/qmlcache
-
     ${cfg.setupScript}
   '';
 
@@ -285,5 +274,20 @@ in
     # To enable user switching, allow sddm to allocate TTYs/displays dynamically.
     services.xserver.tty = null;
     services.xserver.display = null;
+
+    systemd.tmpfiles.rules = [
+      # Prior to Qt 5.9.2, there is a QML cache invalidation bug which sometimes
+      # strikes new Plasma 5 releases. If the QML cache is not invalidated, SDDM
+      # will segfault without explanation. We really tore our hair out for awhile
+      # before finding the bug:
+      # https://bugreports.qt.io/browse/QTBUG-62302
+      # We work around the problem by deleting the QML cache before startup.
+      # This was supposedly fixed in Qt 5.9.2 however it has been reported with
+      # 5.10 and 5.11 as well. The initial workaround was to delete the directory
+      # in the Xsetup script but that doesn't do anything.
+      # Instead we use tmpfiles.d to ensure it gets wiped.
+      # This causes a small but perceptible delay when SDDM starts.
+      "e ${config.users.users.sddm.home}/.cache - - - 0"
+    ];
   };
 }

nixos/modules/system/boot/stage-1.nix

@@ -164,7 +164,7 @@ let
 
       # Strip binaries further than normal.
       chmod -R u+w $out
-      stripDirs "lib bin" "-s"
+      stripDirs "$STRIP" "lib bin" "-s"
 
       # Run patchelf to make the programs refer to the copied libraries.
       find $out/bin $out/lib -type f | while read i; do

pkgs/applications/audio/calf/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, cairo, expat, fftwSinglePrec, fluidsynth, glib
+{ stdenv, fetchurl, fetchpatch, cairo, expat, fftwSinglePrec, fluidsynth, glib
 , gtk2, libjack2, ladspaH , libglade, lv2, pkgconfig }:
 
 stdenv.mkDerivation rec {
@@ -10,6 +10,15 @@ stdenv.mkDerivation rec {
     sha256 = "0dijv2j7vlp76l10s4v8gbav26ibaqk8s24ci74vrc398xy00cib";
   };
 
+  patches = [
+    # Fix memory leak in limiter
+    # https://github.com/flathub/com.github.wwmm.pulseeffects/issues/12
+    (fetchpatch {
+      url = https://github.com/calf-studio-gear/calf/commit/7afdefc0d0489a6227fd10f15843d81dc82afd62.patch;
+      sha256 = "056662iw6hp4ykwk4jyrzg5yarcn17ni97yc060y5kcnzy29ddg6";
+    })
+  ];
+
   buildInputs = [
     cairo expat fftwSinglePrec fluidsynth glib gtk2 libjack2 ladspaH
     libglade lv2 pkgconfig

pkgs/applications/audio/pulseeffects/default.nix

@@ -18,8 +18,12 @@
 , sord
 , sratom
 , libbs2b
+, libsamplerate
+, libsndfile
 , boost
+, fftwFloat
 , calf
+, zita-convolver
 , zam-plugins
 , rubberband
 , mda_lv2
@@ -36,13 +40,13 @@ let
   ];
 in stdenv.mkDerivation rec {
   name = "pulseeffects-${version}";
-  version = "4.1.3";
+  version = "4.1.6";
 
   src = fetchFromGitHub {
     owner = "wwmm";
     repo = "pulseeffects";
     rev = "v${version}";
-    sha256 = "1f89msg8hzaf1pa9w3gaifb88dm0ca2wd81jlz3vr98hm7kxd85k";
+    sha256 = "0fxd1rgf3l667gibd6brfrs8vkq6882w7jql871j5q5ynz1c9j46";
   };
 
   nativeBuildInputs = [
@@ -61,11 +65,16 @@ in stdenv.mkDerivation rec {
     gtk3
     gtkmm3
     gst_all_1.gstreamer
+    gst_all_1.gst-plugins-base
     gst_all_1.gst-plugins-good
     gst_all_1.gst-plugins-bad
     lilv lv2 serd sord sratom
     libbs2b
+    libsamplerate
+    libsndfile
     boost
+    fftwFloat
+    zita-convolver
   ];
 
   postPatch = ''
@@ -74,6 +83,8 @@ in stdenv.mkDerivation rec {
   '';
 
   preFixup = ''
+    addToSearchPath GST_PLUGIN_SYSTEM_PATH_1_0 $out/lib/gstreamer-1.0
+
     gappsWrapperArgs+=(
       --set LV2_PATH "${stdenv.lib.makeSearchPath "lib/lv2" lv2Plugins}"
       --set LADSPA_PATH "${stdenv.lib.makeSearchPath "lib/ladspa" ladspaPlugins}"

pkgs/applications/audio/radiotray-ng/default.nix

@@ -40,13 +40,13 @@ let
 in
 stdenv.mkDerivation rec {
   name = "radiotray-ng-${version}";
-  version = "0.2.2";
+  version = "0.2.3";
 
   src = fetchFromGitHub {
     owner = "ebruck";
     repo = "radiotray-ng";
     rev = "v${version}";
-    sha256 = "0q8k7nsjm6m0r0zs1br60niaqlwvd3myqalb5sqijzanx41aq2l6";
+    sha256 = "1sq7bc0dswv3vv56w527z268ib0pyhdxyf25388vnj1fv0c146wc";
   };
 
   nativeBuildInputs = [ cmake pkgconfig wrapGAppsHook makeWrapper ];

pkgs/applications/editors/emacs-modes/cask/default.nix

@@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, emacs, python }:
 
 stdenv.mkDerivation rec {
-  version = "0.8.1";
+  version = "0.8.4";
   name = "cask-${version}";
 
   src = fetchFromGitHub {
     owner = "cask";
     repo = "cask";
     rev = "v${version}";
-    sha256 = "1sl094adnchjvf189c3l1njawrj5ww1sv5vvjr9hb1ng2rw20z7b";
+    sha256 = "1p37lq8xpyq0rc7phxgsw3b73h8vf9rkpa5959rb5k46w6ps9686";
   };
 
   buildInputs = [ emacs python ];

pkgs/applications/graphics/renderdoc/custom_swig.patch

@@ -1,32 +0,0 @@
-diff --git a/qrenderdoc/CMakeLists.txt b/qrenderdoc/CMakeLists.txt
-index 2df9ffa5..66bafaba 100644
---- a/qrenderdoc/CMakeLists.txt
-+++ b/qrenderdoc/CMakeLists.txt
-@@ -65,16 +65,6 @@ include(ExternalProject)
- # Need bison for swig
- find_package(BISON)
- 
--# Compile our custom SWIG that will do scoped/strong enum classes
--ExternalProject_Add(custom_swig
--    # using an URL to a zip directly so we don't clone the history etc
--    URL ${RENDERDOC_SWIG_PACKAGE}
--    BUILD_IN_SOURCE 1
--    CONFIGURE_COMMAND ./autogen.sh > /dev/null 2>&1
--    COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --with-pcre=yes --prefix=${CMAKE_BINARY_DIR} > /dev/null
--    BUILD_COMMAND $(MAKE) > /dev/null 2>&1
--    INSTALL_COMMAND $(MAKE) install > /dev/null 2>&1)
--
- # Lastly find PySide 2, optionally, for Qt5 Python bindings
- list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}")
- 
-@@ -186,9 +176,8 @@ foreach(in ${swig_interfaces})
-     get_filename_component(swig_file ${in} NAME_WE)
- 
-     add_custom_command(OUTPUT ${swig_file}_python.cxx ${swig_file}.py
--            COMMAND ${CMAKE_BINARY_DIR}/bin/swig -v -Wextra -Werror -O -c++ -python -modern -modernargs -enumclass -fastunpack -py3 -builtin -I${CMAKE_CURRENT_SOURCE_DIR} -I${CMAKE_SOURCE_DIR}/renderdoc/api/replay -outdir ${CMAKE_CURRENT_BINARY_DIR} -o ${CMAKE_CURRENT_BINARY_DIR}/${swig_file}_python.cxx ${CMAKE_CURRENT_SOURCE_DIR}/${in}
-+	    COMMAND $ENV{NIXOS_CUSTOM_SWIG} -v -Wextra -Werror -O -c++ -python -modern -modernargs -enumclass -fastunpack -py3 -builtin -I${CMAKE_CURRENT_SOURCE_DIR} -I${CMAKE_SOURCE_DIR}/renderdoc/api/replay -outdir ${CMAKE_CURRENT_BINARY_DIR} -o ${CMAKE_CURRENT_BINARY_DIR}/${swig_file}_python.cxx ${CMAKE_CURRENT_SOURCE_DIR}/${in}
-             DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/${in}
--            DEPENDS custom_swig
-             DEPENDS ${RDOC_REPLAY_FILES}
-             DEPENDS ${QRD_INTERFACE_FILES})
- 

pkgs/applications/graphics/renderdoc/default.nix

@@ -1,74 +1,62 @@
 { stdenv, fetchFromGitHub, cmake, pkgconfig
-, qtbase, qtx11extras, qtsvg, makeWrapper, python3, bison
+, qtbase, qtx11extras, qtsvg, makeWrapper
-, pcre, vulkan-loader, xorg, autoreconfHook
+, vulkan-loader, xorg
+, python36, bison, pcre, automake, autoconf
 }:
-
 let
-  custom_swig = stdenv.mkDerivation {
+  custom_swig = fetchFromGitHub {
-    name = "renderdoc-custom-swig";
+    owner = "baldurk";
-    src = fetchFromGitHub {
+    repo = "swig";
-      owner = "baldurk";
+    rev = "renderdoc-modified-5";
-      repo = "swig";
+    sha256 = "0ihrxbx56p5wn589fbbsns93fp91sypqdzfxdy7l7v9sf69a41mw";
-      rev = "renderdoc-modified-1";
-      sha256 = "1whymd3vamwnp4jqfc9asls3dw9wsdi21xhm1d2a4vx9nql8if1x";
-    };
-
-    nativeBuildInputs = [ autoreconfHook pcre ];
-
-    autoreconfPhase = ''
-      patchShebangs autogen.sh
-      ./autogen.sh
-    '';
   };
 in
 stdenv.mkDerivation rec {
+  version = "1.0";
   name = "renderdoc-${version}";
-  version = "0.91";
 
   src = fetchFromGitHub {
     owner = "baldurk";
     repo = "renderdoc";
-    rev = "2d8b2cf818746b6a2add54e2fef449398816a40c";
+    rev = "v${version}";
-    sha256 = "07yc3fk7j2nqmrhc4dm3v2pgbc37scd7d28nlzk6v0hw99zck8k0";
+    sha256 = "0l7pjxfrly4llryjnwk42dzx65n78wc98h56qm4yh04ja8fdbx2y";
   };
 
   buildInputs = [
-    qtbase qtsvg xorg.libpthreadstubs xorg.libXdmcp qtx11extras vulkan-loader
+    qtbase qtsvg xorg.libpthreadstubs xorg.libXdmcp qtx11extras vulkan-loader python36
   ];
 
-  nativeBuildInputs = [ cmake makeWrapper pkgconfig python3 bison ];
+  nativeBuildInputs = [ cmake makeWrapper pkgconfig bison pcre automake autoconf ];
+
+  postUnpack = ''
+    cp -r ${custom_swig} swig
+    chmod -R +w swig
+    patchShebangs swig/autogen.sh
+  '';
 
   cmakeFlags = [
     "-DBUILD_VERSION_HASH=${src.rev}"
     "-DBUILD_VERSION_DIST_NAME=NixOS"
-    "-DBUILD_VERSION_DIST_VER=0.91"
+    "-DBUILD_VERSION_DIST_VER=${version}"
     "-DBUILD_VERSION_DIST_CONTACT=https://github.com/NixOS/nixpkgs/tree/master/pkgs/applications/graphics/renderdoc"
-    "-DBUILD_VERSION_DIST_STABLE=ON"
+    "-DBUILD_VERSION_STABLE=ON"
-    # TODO: use this instead of preConfigure once placeholders land
+    # TODO: add once pyside2 is in nixpkgs
-    #"-DVULKAN_LAYER_FOLDER=${placeholder out}/share/vulkan/implicit_layer.d/"
+    #"-DPYSIDE2_PACKAGE_DIR=${python36Packages.pyside2}"
   ];
 
+  # Future work: define these in the above array via placeholders
   preConfigure = ''
     cmakeFlags+=" -DVULKAN_LAYER_FOLDER=$out/share/vulkan/implicit_layer.d/"
+    cmakeFlags+=" -DRENDERDOC_SWIG_PACKAGE=$PWD/../swig"
   '';
 
   preFixup = ''
-    mkdir $out/bin/.bin
-    mv $out/bin/qrenderdoc $out/bin/.bin/qrenderdoc
-    ln -s $out/bin/.bin/qrenderdoc $out/bin/qrenderdoc
     wrapProgram $out/bin/qrenderdoc --suffix LD_LIBRARY_PATH : $out/lib --suffix LD_LIBRARY_PATH : ${vulkan-loader}/lib
-    mv $out/bin/renderdoccmd $out/bin/.bin/renderdoccmd
-    ln -s $out/bin/.bin/renderdoccmd $out/bin/renderdoccmd
     wrapProgram $out/bin/renderdoccmd --suffix LD_LIBRARY_PATH : $out/lib --suffix LD_LIBRARY_PATH : ${vulkan-loader}/lib
   '';
 
-  # Set path to custom swig binary
-  NIXOS_CUSTOM_SWIG = "${custom_swig}/bin/swig";
-
   enableParallelBuilding = true;
 
-  patches = [ ./custom_swig.patch ];
-
   meta = with stdenv.lib; {
     description = "A single-frame graphics debugger";
     homepage = https://renderdoc.org/;

pkgs/applications/misc/gutenberg/default.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   name = "gutenberg-${version}";
-  version = "0.3.1";
+  version = "0.3.4";
 
   src = fetchFromGitHub {
     owner = "Keats";
     repo = "gutenberg";
     rev = "v${version}";
-    sha256 = "03zhbwxp4dbqydiydx0hpp3vpg769zzn5i95h2sl868mpfia8gyd";
+    sha256 = "1v26q1m3bx7mdmmwgd6p601ncf13rr4rrx9s06fiy8vnd0ar1vlf";
   };
 
-  cargoSha256 = "0441lbmxx16aar6fn651ihk3psrx0lk3qdbbyih05xjlkkbk1qxs";
+  cargoSha256 = "0cdy0wvibkpnmlqwxvn02a2k2vqy6zdqzflj2dh6g1cjbz1j8qh5";
 
   nativeBuildInputs = [ cmake ];
   buildInputs = stdenv.lib.optionals stdenv.isDarwin [ CoreServices cf-private ];
@@ -29,7 +29,7 @@ rustPlatform.buildRustPackage rec {
     description = "An opinionated static site generator with everything built-in";
     homepage = https://www.getgutenberg.io;
     license = licenses.mit;
-    maintainers = [];
+    maintainers = with maintainers; [ dywedir ];
     platforms = platforms.all;
   };
 }

pkgs/applications/misc/mucommander/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, gradle_3_5, perl, makeWrapper, jre }:
+{ stdenv, fetchFromGitHub, gradle_3_5, perl, makeWrapper, jre, gsettings-desktop-schemas }:
 
 let
   version = "0.9.2";
@@ -10,7 +10,7 @@ let
     rev = version;
     sha256 = "1fvij0yjjz56hsyddznx7mdgq1zm25fkng3axl03iyrij976z7b8";
   };
-  
+
   postPatch = ''
     # there is no .git anyway
     substituteInPlace build.gradle \
@@ -69,7 +69,9 @@ in stdenv.mkDerivation {
   installPhase = ''
     mkdir $out
     tar xvf build/distributions/mucommander-${version}.tar --directory=$out --strip=1
-    wrapProgram $out/bin/mucommander --set JAVA_HOME ${jre}
+    wrapProgram $out/bin/mucommander \
+      --prefix XDG_DATA_DIRS : ${gsettings-desktop-schemas}/share/gsettings-schemas/${gsettings-desktop-schemas.name} \
+      --set JAVA_HOME ${jre}
   '';
 
   meta = with stdenv.lib; {

pkgs/applications/misc/termite/add_errno_header.patch

@@ -0,0 +1,24 @@
+From 95c90f302c384f410dc92e64468ac7061b57fe2d Mon Sep 17 00:00:00 2001
+From: Michael Hoang <enzime@users.noreply.github.com>
+Date: Fri, 13 Jul 2018 19:03:09 +1000
+Subject: [PATCH] Add errno.h header which isn't always included automatically.
+
+---
+ termite.cc | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/termite.cc b/termite.cc
+index 160fe82..13e2572 100644
+--- a/termite.cc
++++ b/termite.cc
+@@ -21,6 +21,7 @@
+ #include <cstdlib>
+ #include <cstring>
+ #include <cmath>
++#include <errno.h>
+ #include <functional>
+ #include <limits>
+ #include <map>
+-- 
+2.17.1
+

pkgs/applications/misc/termite/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchgit, pkgconfig, vte, gtk3, ncurses, makeWrapper, wrapGAppsHook, symlinkJoin
+{ stdenv, fetchFromGitHub, lib, pkgconfig, vte, gtk3, ncurses, makeWrapper, wrapGAppsHook, symlinkJoin
 , configFile ? null
 }:
 
@@ -7,16 +7,17 @@ let
   termite = stdenv.mkDerivation {
     name = "termite-${version}";
 
-    src = fetchgit {
+    src = fetchFromGitHub {
-      url = "https://github.com/thestinger/termite";
+      owner = "thestinger";
-      rev = "refs/tags/v${version}";
+      repo = "termite";
+      rev = "v${version}";
       sha256 = "02cn70ygl93ghhkhs3xdxn5b1yadc255v3yp8cmhhyzsv5027hvj";
+      fetchSubmodules = true;
     };
 
     # https://github.com/thestinger/termite/pull/516
-    patches = [ ./url_regexp_trailing.patch ];
+    patches = [ ./url_regexp_trailing.patch ./add_errno_header.patch
-
+                ] ++ lib.optional stdenv.isDarwin ./remove_ldflags_macos.patch;
-    postPatch = "sed '1i#include <math.h>' -i termite.cc";
 
     makeFlags = [ "VERSION=v${version}" "PREFIX=" "DESTDIR=$(out)" ];
 

pkgs/applications/misc/termite/remove_ldflags_macos.patch

@@ -0,0 +1,25 @@
+From 1b5a6934635c55472eb7949bd87ab3f45fa1b2f3 Mon Sep 17 00:00:00 2001
+From: Michael Hoang <enzime@users.noreply.github.com>
+Date: Fri, 13 Jul 2018 19:01:51 +1000
+Subject: [PATCH] Remove --as-needed flag from ld to fix compilation on macOS.
+
+---
+ Makefile | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/Makefile b/Makefile
+index b115f42..ab301ba 100644
+--- a/Makefile
++++ b/Makefile
+@@ -29,7 +29,7 @@ ifeq (${CXX}, clang++)
+ 	CXXFLAGS += -Wimplicit-fallthrough
+ endif
+ 
+-LDFLAGS := -s -Wl,--as-needed ${LDFLAGS}
++LDFLAGS := -s -Wl ${LDFLAGS}
+ LDLIBS := ${shell pkg-config --libs ${GTK} ${VTE}}
+ 
+ termite: termite.cc url_regex.hh util/clamp.hh util/maybe.hh util/memory.hh
+-- 
+2.17.1
+

pkgs/applications/networking/browsers/firefox-bin/default.nix

@@ -19,9 +19,11 @@
 , libXScrnSaver
 , libxcb
 , libXcomposite
+, libXcursor
 , libXdamage
 , libXext
 , libXfixes
+, libXi
 , libXinerama
 , libXrender
 , libXt
@@ -104,10 +106,12 @@ stdenv.mkDerivation {
       libX11
       libXScrnSaver
       libXcomposite
+      libXcursor
       libxcb
       libXdamage
       libXext
       libXfixes
+      libXi
       libXinerama
       libXrender
       libXt

pkgs/applications/networking/browsers/firefox/common.nix

@@ -76,7 +76,7 @@ stdenv.mkDerivation (rec {
 
   buildInputs = [
     gtk2 perl zip libIDL libjpeg zlib bzip2
-    dbus dbus-glib pango freetype fontconfig xorg.libXi
+    dbus dbus-glib pango freetype fontconfig xorg.libXi xorg.libXcursor
     xorg.libX11 xorg.libXrender xorg.libXft xorg.libXt file
     nspr libnotify xorg.pixman yasm libGLU_combined
     xorg.libXScrnSaver xorg.scrnsaverproto

pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/default.nix

@@ -84,14 +84,14 @@ stdenv.mkDerivation rec {
     sha256 =
       if debug then
         if arch == "x86_64" then
-          "1ld9ldsqd5vgghpidskxqmlz8gwdyf3mi3wmfdiaabdjxgzbg8sk"
+          "1xa2mcbcxpfrqdf37a98nvvsvyp0bm3lsv21ky3ps9cba8a13z80"
         else
-          "1n96rx95spj4r34amapqr1i1klhv944fpvhdmn7gqjawr2hf36js"
+          "1jgl57ggcszdim51dcr0gsjmrdb2kdvxl0lv5zl83cvxcyz0z4p6"
       else
         if arch == "x86_64" then
           "0331r5af4zrvwc4h7dp5qyy91dfam5z03yjggls3x04i10nz5myw"
         else
-          "01ibzqzlscpkfqp33bx7qcpz6gfqp4dq9ny3zasvjhi5xqd78j1k";
+          "011cf0kycs4ih45l23bp6rr2vm7w7jaj4pjvmqwjax4xrb5pzkic";
   };
 
   nativeBuildInputs = [ unzip ];

pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/standalone.nix

@@ -65,9 +65,9 @@ stdenv.mkDerivation rec {
         "https://fpdownload.macromedia.com/pub/flashplayer/updaters/30/flash_player_sa_linux.x86_64.tar.gz";
     sha256 =
       if debug then
-        "0snkhs9w192azgv3nykxmgb47z395yrx7faxshasmc7abvvnfpx1"
+        "1plmhv1799j0habmyxy7zhvilh823djmg4i387s6qifr5iv66pax"
       else
-        "1wgcsbm9w46sp8347agd5m05x3xrki8vi6pf208ifihljw04hbx3";
+        "13cb7sca5mw5b1iiimyxbfxwpmdh7aya8rnlhkv3fgk5a1jwrxqr";
   };
 
   nativeBuildInputs = [ unzip ];

pkgs/applications/networking/charles/default.nix

@@ -0,0 +1,48 @@
+{ stdenv, fetchurl, makeDesktopItem, jre, makeWrapper }:
+
+let
+  desktopItem = makeDesktopItem {
+    categories = "Network;Development;WebDevelopment;Java;";
+    desktopName = "Charles";
+    exec = "charles %F";
+    genericName  = "Web Debugging Proxy";
+    icon = "charles-proxy";
+    mimeType = "application/x-charles-savedsession;application/x-charles-savedsession+xml;application/x-charles-savedsession+json;application/har+json;application/vnd.tcpdump.pcap;application/x-charles-trace";
+    name = "Charles";
+    startupNotify = "true";
+  };
+
+in stdenv.mkDerivation rec {
+  name = "charles-${version}";
+  version = "4.2.6";
+
+  src = fetchurl {
+    url = "https://www.charlesproxy.com/assets/release/${version}/charles-proxy-${version}.tar.gz";
+    sha256 = "1hjfimyr9nnbbxadwni02d2xl64ybarh42l1g6hlslq5qwl8ywzb";
+  };
+
+  buildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    makeWrapper ${jre}/bin/java $out/bin/charles \
+      --add-flags "-Xmx1024M -Dcharles.config='~/.charles.config' -jar $out/share/java/charles.jar"
+
+    for fn in lib/*.jar; do
+      install -D -m644 $fn $out/share/java/$(basename $fn)
+    done
+
+    mkdir -p $out/share/applications
+    ln -s ${desktopItem}/share/applications/* $out/share/applications/
+
+    mkdir -p $out/share/icons
+    cp -r icon $out/share/icons/hicolor
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Web Debugging Proxy";
+    homepage = https://www.charlesproxy.com/;
+    maintainers = [ maintainers.kalbasit ];
+    license = stdenv.lib.licenses.unfree;
+    platforms = stdenv.lib.platforms.linux ++ stdenv.lib.platforms.darwin;
+  };
+}

pkgs/applications/networking/cluster/terraform-provider-ibm/default.nix

@@ -12,7 +12,7 @@
 
 buildGoPackage rec {
   name = "terraform-provider-ibm-${version}";
-  version = "0.11.0";
+  version = "0.11.1";
 
   goPackagePath = "github.com/terraform-providers/terraform-provider-ibm";
   subPackages = [ "./" ];
@@ -20,7 +20,7 @@ buildGoPackage rec {
   src = fetchFromGitHub {
     owner = "IBM-Cloud";
     repo = "terraform-provider-ibm";
-    sha256 = "0zgzzs2l9p06angqw6vjpkd88gcn2mswmmwycc31ihkglzs6yw2p";
+    sha256 = "1vp1kzadfkacn6c4illxjra8yki1fx7h77b38fixkcvc79mzasmv";
     rev = "v${version}";
   };
 

pkgs/applications/networking/instant-messengers/signal-desktop/default.nix

@@ -40,11 +40,11 @@ let
 
 in stdenv.mkDerivation rec {
   name = "signal-desktop-${version}";
-  version = "1.14.0";
+  version = "1.14.1";
 
   src = fetchurl {
     url = "https://updates.signal.org/desktop/apt/pool/main/s/signal-desktop/signal-desktop_${version}_amd64.deb";
-    sha256 = "1f76dzm9qq12i4s95c51d9s923n69y8cbg8yz79qjpd6k30j8vkq";
+    sha256 = "1f54azqdfqa2yrzlp9b7pz7nswl5n3pgln38yxcvb3y5k6x0ljqp";
   };
 
   phases = [ "unpackPhase" "installPhase" ];

pkgs/applications/networking/instant-messengers/zoom-us/default.nix

@@ -1,16 +1,18 @@
-{ stdenv, fetchurl, system, makeWrapper, makeDesktopItem, autoPatchelfHook
+{ stdenv, fetchurl, system, makeWrapper, makeDesktopItem, autoPatchelfHook, env
 # Dynamic libraries
 , dbus, glib, libGL, libX11, libXfixes, libuuid, libxcb, qtbase, qtdeclarative
-, qtlocation, qtquickcontrols2, qtscript, qtwebchannel, qtwebengine
+, qtimageformats, qtlocation, qtquickcontrols, qtquickcontrols2, qtscript, qtsvg
+, qttools, qtwayland, qtwebchannel, qtwebengine
 # Runtime
-, libjpeg_turbo, pciutils, procps, qtimageformats
+, coreutils, libjpeg_turbo, pciutils, procps, utillinux
 , pulseaudioSupport ? true, libpulseaudio ? null
 }:
 
 assert pulseaudioSupport -> libpulseaudio != null;
 
 let
-  inherit (stdenv.lib) concatStringsSep makeBinPath optional optionalString;
+  inherit (stdenv.lib) concatStringsSep makeBinPath makeLibraryPath
+    makeSearchPath optional optionalString;
 
   version = "2.2.128200.0702";
   srcs = {
@@ -20,6 +22,13 @@ let
     };
   };
 
+  qtDeps = [
+    qtbase qtdeclarative qtlocation qtquickcontrols qtquickcontrols2 qtscript
+    qtwebchannel qtwebengine qtimageformats qtsvg qttools qtwayland
+  ];
+
+  qtEnv = env "zoom-us-qt-${qtbase.version}" qtDeps;
+
 in stdenv.mkDerivation {
   name = "zoom-us-${version}";
 
@@ -28,10 +37,8 @@ in stdenv.mkDerivation {
   nativeBuildInputs = [ autoPatchelfHook makeWrapper ];
 
   buildInputs = [
-    dbus glib libGL libX11 libXfixes libuuid libxcb qtbase qtdeclarative
+    dbus glib libGL libX11 libXfixes libuuid libxcb qtEnv libjpeg_turbo
-    qtlocation qtquickcontrols2 qtscript qtwebchannel qtwebengine
+  ] ++ qtDeps;
-    libjpeg_turbo
-  ];
 
   runtimeDependencies = optional pulseaudioSupport libpulseaudio;
 
@@ -46,7 +53,6 @@ in stdenv.mkDerivation {
         "ZXMPPROOT.cer"
         "ZoomLauncher"
         "config-dump.sh"
-        "qtdiag"
         "timezones"
         "translations"
         "version.txt"
@@ -67,11 +73,10 @@ in stdenv.mkDerivation {
       # TODO Patch this somehow; tries to dlopen './libturbojpeg.so' from cwd
       ln -s $(readlink -e "${libjpeg_turbo.out}/lib/libturbojpeg.so") $packagePath/libturbojpeg.so
 
+      ln -s ${qtEnv}/bin/qt.conf $packagePath
+
       makeWrapper $packagePath/zoom $out/bin/zoom-us \
-        --prefix PATH : "${makeBinPath [ pciutils procps ]}" \
+        --prefix PATH : "${makeBinPath [ coreutils glib.dev pciutils procps qttools.dev utillinux ]}" \
-        --set QSG_INFO 1 \
-        --set QT_QPA_PLATFORM_PLUGIN_PATH ${qtbase.bin}/lib/qt-${qtbase.qtCompatVersion}/plugins/platforms \
-        --set QT_PLUGIN_PATH ${qtbase.bin}/${qtbase.qtPluginPrefix}:${qtimageformats}/${qtbase.qtPluginPrefix} \
         --run "cd $packagePath"
 
       runHook postInstall

pkgs/applications/science/chemistry/octopus/default.nix

@@ -1,9 +1,9 @@
 { stdenv, fetchurl, symlinkJoin, gfortran, perl, procps
-, libyaml, libxc, fftw, openblas, gsl
+, libyaml, libxc, fftw, openblas, gsl, netcdf, arpack
 }:
 
 let
-  version = "7.3";
+  version = "8.1";
   fftwAll = symlinkJoin { name ="ftw-dev-out"; paths = [ fftw.dev fftw.out ]; };
 
 in stdenv.mkDerivation {
@@ -11,11 +11,11 @@ in stdenv.mkDerivation {
 
   src = fetchurl {
     url = "http://www.tddft.org/programs/octopus/down.php?file=${version}/octopus-${version}.tar.gz";
-    sha256 = "0hnpqjjxdxh2ggf6ckrsy4hs9iglnazscb4siczddvmysi4kv15d";
+    sha256 = "0rxwvcp22364nnhwhqlr38w4rwv1yl60snxi2f8nqdflx1143n10";
   };
 
   nativeBuildInputs = [ perl procps fftw.dev ];
-  buildInputs = [ libyaml gfortran libxc openblas gsl fftw.out ];
+  buildInputs = [ libyaml gfortran libxc openblas gsl fftw.out netcdf arpack ];
 
   configureFlags = ''
     --with-yaml-prefix=${libyaml}
@@ -37,6 +37,8 @@ in stdenv.mkDerivation {
     patchShebangs testsuite/oct-run_testsuite.sh
   '';
 
+  enableParallelBuilding = true;
+
   meta = with stdenv.lib; {
     description = "Real-space time dependent density-functional theory code";
     homepage = http://octopus-code.org;

pkgs/applications/science/logic/z3/default.nix

@@ -27,9 +27,7 @@ stdenv.mkDerivation rec {
     mv $out/lib          $lib/lib
     mv $out/include      $dev/include
 
-    # clean up a copy of libz3.so and symlink it instead
+    ln -sf $lib/lib/libz3${stdenv.hostPlatform.extensions.sharedLibrary} $python/${python.sitePackages}/z3/lib/libz3${stdenv.hostPlatform.extensions.sharedLibrary}
-    rm $python/${python.sitePackages}/z3/lib/libz3.so
-    ln -s $lib/lib/libz3.so $python/${python.sitePackages}/z3/lib/libz3.so
   '';
 
   outputs = [ "out" "lib" "dev" "python" ];

pkgs/applications/science/math/sage/sage-src.nix

@@ -84,6 +84,12 @@ stdenv.mkDerivation rec {
   ];
 
   packageUpgradePatches = [
+    (fetchpatch {
+      name = "cypari2-1.2.1.patch";
+      url = "https://git.sagemath.org/sage.git/patch/?h=62fe6eb15111327d930336d4252d5b23cbb22ab9";
+      sha256 = "1xax7vvs8h4xip16xcsp47xdb6lig6f2r3pl8cksvlz8lhgbyxh2";
+    })
+
     # matplotlib 2.2.2 deprecated `normed` (replaced by `density`).
     # This patch only ignores the warning. It would be equally easy to fix it
     # (by replacing all mentions of `normed` by `density`), but its better to

pkgs/applications/video/mkvtoolnix/default.nix

@@ -12,13 +12,13 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "mkvtoolnix-${version}";
-  version = "24.0.0";
+  version = "25.0.0";
 
   src = fetchFromGitLab {
     owner  = "mbunkus";
     repo   = "mkvtoolnix";
     rev    = "release-${version}";
-    sha256 = "0r6v7n4wq1ivjcfs4br5ywz2f0jbwxrharfcjmycnbjsckz1l7ps";
+    sha256 = "04m57719q7q0h0gcj1b2bh8xbdcl5bijic4hw71xf9xd19a95k78";
   };
 
   nativeBuildInputs = [

pkgs/data/misc/iana-etc/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "iana-etc-${version}";
-  version = "20180405";
+  version = "20180711";
 
   src = fetchurl {
     url = "https://github.com/Mic92/iana-etc/releases/download/${version}/iana-etc-${version}.tar.gz";
-    sha256 = "0x6i95arrc4lcq2il3r05hbnd9vsi87z4yc8s3agkvbj74d6hfhj";
+    sha256 = "0xigkz6pcqx55px7fap7j6p3hz27agv056crbl5pgfcdix7y8z26";
   };
 
   installPhase = ''

pkgs/desktops/gnome-3/apps/gnome-logs/default.nix

@@ -1,28 +1,15 @@
-{ stdenv, fetchurl, fetchpatch, meson, ninja, pkgconfig, gnome3, glib, gtk3, wrapGAppsHook, desktop-file-utils
+{ stdenv, fetchurl, meson, ninja, pkgconfig, gnome3, glib, gtk3, wrapGAppsHook, desktop-file-utils
 , gettext, itstool, libxml2, libxslt, docbook_xsl, docbook_xml_dtd_43, systemd, python3 }:
 
 stdenv.mkDerivation rec {
   name = "gnome-logs-${version}";
-  version = "3.28.3";
+  version = "3.28.5";
 
   src = fetchurl {
     url = "mirror://gnome/sources/gnome-logs/${gnome3.versionBranch version}/${name}.tar.xz";
-    sha256 = "1bpg8172f16sgbhsn2sis3xh2ylrv8vj7j12xdxkmsmfh2k2bqfy";
+    sha256 = "0zw6nx1hckv46hn978g57anp4zq4alvz9dpwibgx02wb6gq1r23a";
   };
 
-  patches = [
-    # Fix post_install script
-    (fetchpatch {
-      url = https://gitlab.gnome.org/GNOME/gnome-logs/commit/2f498464ac539fdf98199294bfb9205436b9c323.patch;
-      sha256 = "1v6d8zgd31waliwlvk5xlfjap5h84bpqb1az0wdjm4c2a53iiwlp";
-    })
-    # Fix a typo in manpage generation
-    (fetchpatch {
-      url = https://gitlab.gnome.org/GNOME/gnome-logs/commit/02b782fcd64d4773e2dadbdb9ea74bf3923003b3.patch;
-      sha256 = "1a8zcp62shspw45s0dvi2iv83qppz4hcw31id6zlwq0dp94vvb46";
-    })
-  ];
-
   mesonFlags = [
     "-Dtests=true"
     "-Dman=true"

pkgs/desktops/gnome-3/core/gucharmap/default.nix

@@ -1,41 +1,55 @@
-{ stdenv, intltool, fetchurl, pkgconfig, gtk3, defaultIconTheme
+{ stdenv, intltool, fetchFromGitLab, pkgconfig, gtk3, defaultIconTheme
-, glib, desktop-file-utils, bash, appdata-tools
+, glib, desktop-file-utils, bash, appdata-tools, gtk-doc, autoconf, automake, libtool
 , wrapGAppsHook, gnome3, itstool, libxml2
 , callPackage, unzip, gobjectIntrospection }:
 
-stdenv.mkDerivation rec {
+let
+  unicode-data = callPackage ./unicode-data.nix {};
+in stdenv.mkDerivation rec {
   name = "gucharmap-${version}";
-  version = "10.0.4";
+  version = "11.0.1";
 
-  src = fetchurl {
+  src = fetchFromGitLab {
-    url = "mirror://gnome/sources/gucharmap/${gnome3.versionBranch version}/${name}.tar.xz";
+    domain = "gitlab.gnome.org";
-    sha256 = "00gh3lll6wykd2qg1lrj05a4wvscsypmrx7rpb6jsbvb4scnh9mv";
+    owner = "GNOME";
+    repo = "gucharmap";
+    rev = version;
+    sha256 = "13iw4fa6mv8vi8bkwk0bbhamnzbaih0c93p4rh07khq6mxa6hnpi";
   };
 
-  passthru = {
-    updateScript = gnome3.updateScript { packageName = "gucharmap"; };
-  };
-
-  doCheck = true;
-
-  preConfigure = "patchShebangs gucharmap/gen-guch-unicode-tables.pl";
-
   nativeBuildInputs = [
     pkgconfig wrapGAppsHook unzip intltool itstool appdata-tools
+    autoconf automake libtool gtk-doc
     gnome3.yelp-tools libxml2 desktop-file-utils gobjectIntrospection
   ];
 
   buildInputs = [ gtk3 glib gnome3.gsettings-desktop-schemas defaultIconTheme ];
 
-  unicode-data = callPackage ./unicode-data.nix {};
+  configureFlags = [
+    "--with-unicode-data=${unicode-data}"
+  ];
 
-  configureFlags = "--with-unicode-data=${unicode-data}";
+  doCheck = true;
+
+  postPatch = ''
+    patchShebangs gucharmap/gen-guch-unicode-tables.pl
+  '';
+
+  preConfigure = ''
+    NOCONFIGURE=1 ./autogen.sh
+  '';
+
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = "gucharmap";
+    };
+  };
 
   meta = with stdenv.lib; {
-    homepage = https://wiki.gnome.org/Apps/Gucharmap;
     description = "GNOME Character Map, based on the Unicode Character Database";
-    maintainers = gnome3.maintainers;
+    homepage = https://wiki.gnome.org/Apps/Gucharmap;
     license = licenses.gpl3;
+    maintainers = gnome3.maintainers;
     platforms = platforms.linux;
   };
 }

pkgs/desktops/gnome-3/core/gucharmap/unicode-data.nix

@@ -1,30 +1,31 @@
 { fetchurl, stdenv, gnome3 }:
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
-  name = "unicode-data-10.0.0";
+  name = "unicode-data-${version}";
+  version = "11.0.0";
   srcs = [
     (fetchurl {
-      url = "http://www.unicode.org/Public/10.0.0/ucd/Blocks.txt";
+      url = "http://www.unicode.org/Public/${version}/ucd/Blocks.txt";
-      sha256 = "19zf2kd198mcv1paa194c1zf36hay1irbxssi35yi2pd8ad69qas";
+      sha256 = "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b";
     })
     (fetchurl {
-      url = "http://www.unicode.org/Public/10.0.0/ucd/DerivedAge.txt";
+      url = "http://www.unicode.org/Public/${version}/ucd/DerivedAge.txt";
-      sha256 = "1h9p1g0wnh686l6cqar7cmky465vwc6vjzzn1s7v0i9zcjaqkr4h";
+      sha256 = "0rlqqd0b1sqbzvrj29dwdizx8lyvrbfirsnn8za9lb53x5fml4gb";
     })
     (fetchurl {
-      url = "http://www.unicode.org/Public/10.0.0/ucd/NamesList.txt";
+      url = "http://www.unicode.org/Public/${version}/ucd/NamesList.txt";
-      sha256 = "0gvpcyq852rnlqmx4y5i1by7bavvcw6rj40i54w48yc7xr3zmgd1";
+      sha256 = "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8";
     })
     (fetchurl {
-      url = "http://www.unicode.org/Public/10.0.0/ucd/Scripts.txt";
+      url = "http://www.unicode.org/Public/${version}/ucd/Scripts.txt";
-      sha256 = "0b9prz2hs6w61afqaplcxnv115f8yk4d5hn9dc5hks8nqpj28bnh";
+      sha256 = "1mbnvf97nwa3pvyzx9nd2wa94f8s0npg9740kic2p2ag7jmc1wz9";
     })
     (fetchurl {
-      url = "http://www.unicode.org/Public/10.0.0/ucd/UnicodeData.txt";
+      url = "http://www.unicode.org/Public/${version}/ucd/UnicodeData.txt";
-      sha256 = "1cfak1j753zcrbgixwgppyxhm4w8vda8vxhqymi7n5ljfi6kwhjj";
+      sha256 = "16b0jzvvzarnlxdvs2izd5ia0ipbd87md143dc6lv6xpdqcs75s9";
     })
     (fetchurl {
-      url = "http://www.unicode.org/Public/10.0.0/ucd/Unihan.zip";
+      url = "http://www.unicode.org/Public/${version}/ucd/Unihan.zip";
-      sha256 = "199kz6laypkvc0ykms6d7bkb571jmpds39sv2p7kd5jjm1ij08q1";
+      sha256 = "0cy8gxb17ksi5h4ysypk4c09z61am1svjrvg97hm5m5ccjfrs1vj";
     })
   ];
   phases = "installPhase";

pkgs/desktops/gnome-3/misc/geary/default.nix

@@ -6,14 +6,14 @@
 
 let
   pname = "geary";
-  version = "0.12.2";
+  version = "0.12.3";
 in
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${name}.tar.xz";
-    sha256 = "09j5gh4zm49fcg2ycvy00dkkw69rfppqwc3lqdi4994hry4jivx9";
+    sha256 = "18zzjzs075zja00xpnyvjrrdzm54icdhfw4ywhpr6rqfcpnzifw7";
   };
 
   nativeBuildInputs = [ vala_0_40 intltool pkgconfig wrapGAppsHook cmake ninja desktop-file-utils gnome-doc-utils gobjectIntrospection ];

pkgs/desktops/mate/libmatekbd/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "libmatekbd-${version}";
-  version = "1.20.2";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "1l1zbphs4snswf4bkrwkk6gsmb44bdhymcfgaaspzbrcmw3y7hr1";
+    sha256 = "0xi5ds2psbf0qb0363ljxz5m9xxh1hr2hcn8zv6ni6mdqsqnkajz";
   };
 
   nativeBuildInputs = [ pkgconfig intltool ];

pkgs/desktops/mate/libmatemixer/default.nix

@@ -6,11 +6,11 @@
 
 stdenv.mkDerivation rec {
   name = "libmatemixer-${version}";
-  version = "1.20.1";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "00p67mi0flsbgn15qpwq60rzf917s5islbmhirbvz6npcvv0d493";
+    sha256 = "1376x3rlisrc6hsz6yzi637msplmacxryyqnrsgfc580knp1nrvm";
   };
 
   nativeBuildInputs = [ pkgconfig intltool ];

pkgs/desktops/mate/libmateweather/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "libmateweather-${version}";
-  version = "1.20.1";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "0bp1nn3b5gf5nqrdwl43fxbb82j74s3x8jkmp40ilv2qpc2mxwr1";
+    sha256 = "1vj2pgry6wdscdcpwwagqlsjf8rkh4id67iw7d9qk1pfbhb2sznl";
   };
 
   nativeBuildInputs = [ pkgconfig intltool ];

pkgs/desktops/mate/marco/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "marco-${version}";
-  version = "1.20.2";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "1fn0yfqjp44gr4kly96qjsd73x06z1xyw6bpyhh09kdqwd80rgiy";
+    sha256 = "1vg3dl7kqhzgspa2ykyql4j3bpki59769qrkakqfdcavb9j5c877";
   };
 
   nativeBuildInputs = [

pkgs/desktops/mate/mate-applets/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-applets-${version}";
-  version = "1.20.2";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "0c860yxbphpvci281gj78ipw1rvcka4rr0bxwvg0nkpangdhj9ls";
+    sha256 = "0jr66xrwjrlyh4hz6h5axh96pgxm8n1xyc0rmggah2fijs940rsb";
   };
 
   nativeBuildInputs = [

pkgs/desktops/mate/mate-calc/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-calc-${version}";
-  version = "1.20.2";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "1ghz03j9lfgrjrh8givsw83dpbkw4wlhq4ar3r5g1bf1z636jlx0";
+    sha256 = "07mmc99wwgqbp15zrr6z7iz0frc388z19jwk28ymyzgn6bcc9cn6";
   };
 
   nativeBuildInputs = [

pkgs/desktops/mate/mate-menus/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-menus-${version}";
-  version = "1.20.1";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "1p8pkw6aby2hq2liqrnsf3lvyn2jqamfbs83fv6q7clw5w179sy6";
+    sha256 = "168f7jgm4kbnx92xh3iqvvrgpkv1q862xg27zxg40nkz5xhk95hx";
   };
 
   nativeBuildInputs = [ pkgconfig intltool ];

pkgs/desktops/mate/mate-power-manager/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-power-manager-${version}";
-  version = "1.20.2";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "1z754jxnwashwxxfg3cxb9ifbqyjxgavzzwy2mjnzl6z7k95hvjh";
+    sha256 = "1l7rxv16j95w26igs4n7fdfv5hqm91b9ddc1lw5m26s42nkzzf85";
   };
 
   buildInputs = [

pkgs/desktops/mate/mate-sensors-applet/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-sensors-applet-${version}";
-  version = "1.20.2";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "0khxzwjjf2gp9ma6ji0ynvvqlw6hhr8j4gff9klkrn60xbg5h16b";
+    sha256 = "1l84hfxz5qzipchxxi5whccq5d0kg9c8fxisar8pbckl6763b4dx";
   };
 
   nativeBuildInputs = [

pkgs/desktops/mate/mate-settings-daemon/default.nix

@@ -4,11 +4,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-settings-daemon-${version}";
-  version = "1.20.3";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "018f2yg4jd6hy0z7ks0s3jyjgpyi3vhd9j61951v5lb1x8ckzxhk";
+    sha256 = "1k0xbwxpv3wfl7z3hgaf2ylzaz3aky4j7awdy8cfgxr0d6nqhp3w";
   };
 
   nativeBuildInputs = [

pkgs/desktops/mate/mate-system-monitor/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-system-monitor-${version}";
-  version = "1.20.1";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "1a68il7pbch5028fm2caxyjkfrdc6ixhqnaspbwfziw6y8p9bscn";
+    sha256 = "0filf6qyw4fk45br3cridbqdngwl525z49zn36r7q4agzhny4phz";
   };
 
   nativeBuildInputs = [

pkgs/desktops/mate/mate-terminal/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-terminal-${version}";
-  version = "1.20.1";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "0yfr857mpxy35zzdmicvd7mpwka8s1h0rqagfjqc2p1gv4a7ka97";
+    sha256 = "15vx7b5nbjbym22pz3l3cyqhv4dnd6vl2hb56xhwq625aw2a7chv";
   };
 
   buildInputs = [

pkgs/desktops/mate/mate-utils/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-utils-${version}";
-  version = "1.20.1";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "1kr0612h6r2gj3yg4ccyzr844lh640cd4wdj3gl8qzqikjx0n7ka";
+    sha256 = "0q05zzxgwwk7af05yzcjixjd8hi8cqykirj43g60ikhzym009n4q";
   };
 
   nativeBuildInputs = [

pkgs/desktops/xfce/panel-plugins/xfce4-hardware-monitor-plugin.nix

@@ -5,11 +5,11 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname  = "xfce4-hardware-monitor-plugin";
-  version = "1.5.0";
+  version = "1.6.0";
 
   src = fetchurl {
     url = "https://git.xfce.org/panel-plugins/${pname}/snapshot/${name}.tar.bz2";
-    sha256 = "0sqvisr8gagpywq9sfyzqw37hxmj54ii89j5s2g8hx8bng5a98z1";
+    sha256 = "0xg5har11fk1wmdymydxlbk1z8aa39j8k0p4gzw2iqslv3n0zf7b";
   };
 
   nativeBuildInputs = [

pkgs/development/beam-modules/hex-registry-snapshot.nix

@@ -2,15 +2,14 @@
 
 stdenv.mkDerivation rec {
     name = "hex-registry";
-    rev = "9f736e7";
+    rev = "11d7a24e9f53f52490ce255a6248e71128e73aa1";
-    version = "0.0.0+build.${rev}";
+    version = "20180712.${rev}";
 
-    # src = /home/gleber/code/erl/hex-pm-registry-snapshots;
     src = fetchFromGitHub {
-        owner = "erlang-nix";
-        repo = "hex-pm-registry-snapshots";
         inherit rev;
-        sha256 = "1xiw5yifyk3bbmr0cr82y1nc4c6zk11f6azdv07glb7yrgccrv79";
+        owner  = "erlang-nix";
+        repo   = "hex-pm-registry-snapshots";
+        sha256 = "0dbpcrdh6jqmvnm1ysmy7ixyc95vnbqmikyx5kk77qwgyd43fqgi";
     };
 
     installPhase = ''

pkgs/development/compilers/go/1.10.nix

@@ -34,6 +34,8 @@ stdenv.mkDerivation rec {
     sha256 = "0i89298dgnmpmam3ifkm0ax266vvbq1yz7wfw8wwrcma0szrbrnb";
   };
 
+  GOCACHE = "off";
+
   # perl is used for testing go vet
   nativeBuildInputs = [ perl which pkgconfig patch makeWrapper procps ];
   buildInputs = [ cacert pcre ]

pkgs/development/compilers/openjdk/10.nix

@@ -142,7 +142,7 @@ let
 
     # FIXME: this is unnecessary once the multiple-outputs branch is merged.
     preFixup = ''
-      prefix=$jre stripDirs "$stripDebugList" "''${stripDebugFlags:--S}"
+      prefix=$jre stripDirs "$STRIP" "$stripDebugList" "''${stripDebugFlags:--S}"
       patchELF $jre
       propagatedBuildInputs+=" $jre"
 

pkgs/development/compilers/openjdk/8.nix

@@ -206,7 +206,7 @@ let
 
     # FIXME: this is unnecessary once the multiple-outputs branch is merged.
     preFixup = ''
-      prefix=$jre stripDirs "$stripDebugList" "''${stripDebugFlags:--S}"
+      prefix=$jre stripDirs "$STRIP" "$stripDebugList" "''${stripDebugFlags:--S}"
       patchELF $jre
       propagatedBuildInputs+=" $jre"
 

pkgs/development/libraries/audio/zita-convolver/default.nix

@@ -15,11 +15,14 @@ stdenv.mkDerivation rec {
     sed -e "s@ldconfig@@" -i Makefile
   '';
 
-  installPhase = ''
+  makeFlags = [
-    make PREFIX="$out" SUFFIX="" install
+    "PREFIX=$(out)"
+    "SUFFIX="
+  ];
 
+  postInstall = ''
     # create lib link for building apps
-    ln -s $out/lib/libzita-convolver.so.$version $out/lib/libzita-convolver.so.3
+    ln -s $out/lib/libzita-convolver.so.${version} $out/lib/libzita-convolver.so.${stdenv.lib.versions.major version}
   '';
 
   meta = {

pkgs/development/libraries/ffmpeg-full/default.nix

@@ -232,11 +232,11 @@ assert nvenc -> nvidia-video-sdk != null && nonfreeLicensing;
 
 stdenv.mkDerivation rec {
   name = "ffmpeg-full-${version}";
-  version = "4.0";
+  version = "4.0.1";
 
   src = fetchurl {
     url = "https://www.ffmpeg.org/releases/ffmpeg-${version}.tar.xz";
-    sha256 = "0gx4ngnhi5glmxh38603qy5n6vq8bl1cr4sqd1xff95i82pmv57d";
+    sha256 = "1vn04n0n46zdxq14cma3w8ml2ckh5jxwlybsc4xmvcqdqq0mqpv0";
   };
 
   prePatch = ''

pkgs/development/libraries/ffmpeg/3.4.nix

@@ -6,7 +6,7 @@
 
 callPackage ./generic.nix (args // rec {
   version = "${branch}";
-  branch = "3.4.2";
+  branch = "3.4.3";
-  sha256 = "0nkq4451masmzlx3p4vprqwc0sl2iwqxbzjrngmvj29q4azp00zb";
+  sha256 = "0s2p2bcrywlya4wjlyzi1382vngkiijjvjr6ms64xww5jplwmhmk";
   darwinFrameworks = [ Cocoa CoreMedia ];
 })

pkgs/development/libraries/ffmpeg/4.nix

@@ -6,7 +6,7 @@
 
 callPackage ./generic.nix (args // rec {
   version = "${branch}";
-  branch = "4.0";
+  branch = "4.0.1";
-  sha256 = "1f3k8nz5ag6szsfhlrz66qm8s1yxk1vphqvcfr4ps4690vckk2ii";
+  sha256 = "0w0nq98sn5jwx982wzg3vfrxv4p0k1fvsksiz9az0rpvwyqr3rby";
   darwinFrameworks = [ Cocoa CoreMedia ];
 })

pkgs/development/libraries/ffmpeg/generic.nix

@@ -148,7 +148,7 @@ stdenv.mkDerivation rec {
       "--disable-stripping"
     # Disable mmx support for 0.6.90
       (verFix null "0.6.90" "--disable-mmx")
-  ] ++ optionals (stdenv.hostPlatform == stdenv.buildPlatform) [
+  ] ++ optionals (stdenv.hostPlatform != stdenv.buildPlatform) [
       "--cross-prefix=${stdenv.cc.targetPrefix}"
       "--enable-cross-compile"
   ] ++ optional stdenv.cc.isClang "--cc=clang";
@@ -170,9 +170,15 @@ stdenv.mkDerivation rec {
 
   doCheck = false; # fails
 
+  # ffmpeg 3+ generates pkg-config (.pc) files that don't have the
+  # form automatically handled by the multiple-outputs hooks.
   postFixup = ''
     moveToOutput bin "$bin"
     moveToOutput share/ffmpeg/examples "$doc"
+    for pc in ''${!outputDev}/lib/pkgconfig/*.pc; do
+      substituteInPlace $pc \
+        --replace "includedir=$out" "includedir=''${!outputInclude}"
+    done
   '';
 
   installFlags = [ "install-man" ];

pkgs/development/libraries/libebml/default.nix

@@ -1,19 +1,27 @@
-{ stdenv, fetchurl }:
+{ stdenv, fetchFromGitHub, cmake, pkgconfig }:
 
 stdenv.mkDerivation rec {
-  name = "libebml-1.3.5";
+  name = "libebml-${version}";
+  version = "1.3.6";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "https://dl.matroska.org/downloads/libebml/${name}.tar.xz";
+    owner  = "Matroska-Org";
-    sha256 = "005a0ipqnfbsq47zrc61zszi439jw32q5xd6dc1jyb3lc0zl266q";
+    repo   = "libebml";
+    rev    = "release-${version}";
+    sha256 = "0fl8d35ywj9id93yp78qlxy7j81kjri957agq40r420kmwac3dzs";
   };
 
+  nativeBuildInputs = [ cmake pkgconfig ];
+
+  cmakeFlags = [
+    "-DBUILD_SHARED_LIBS=YES"
+  ];
+
   meta = with stdenv.lib; {
     description = "Extensible Binary Meta Language library";
-    license = licenses.lgpl21;
     homepage = https://dl.matroska.org/downloads/libebml/;
-    maintainers = [ maintainers.spwhitt ];
+    license = licenses.lgpl21;
+    maintainers = with maintainers; [ spwhitt ];
     platforms = platforms.unix;
   };
 }
-

pkgs/development/libraries/libmatroska/default.nix

@@ -1,23 +1,30 @@
-{ stdenv, fetchurl, pkgconfig, libebml }:
+{ stdenv, fetchFromGitHub, cmake, pkgconfig
+, libebml }:
 
 stdenv.mkDerivation rec {
-  name = "libmatroska-1.4.8";
+  name = "libmatroska-${version}";
+  version = "1.4.9";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "https://dl.matroska.org/downloads/libmatroska/${name}.tar.xz";
+    owner  = "Matroska-Org";
-    sha256 = "14n9sw974prr3yp4yjb7aadi6x2yz5a0hjw8fs3qigy5shh2piyq";
+    repo   = "libmatroska";
+    rev    = "release-${version}";
+    sha256 = "1hfrcpvmyqnvdkw8rz1z20zw7fpnjyl5h0g9ky7k6y1a44b1fz86";
   };
 
-  nativeBuildInputs = [ pkgconfig ];
+  nativeBuildInputs = [ cmake pkgconfig ];
 
   buildInputs = [ libebml ];
 
+  cmakeFlags = [
+    "-DBUILD_SHARED_LIBS=YES"
+  ];
+
   meta = with stdenv.lib; {
     description = "A library to parse Matroska files";
     homepage = https://matroska.org/;
     license = licenses.lgpl21;
-    maintainers = [ maintainers.spwhitt ];
+    maintainers = with maintainers; [ spwhitt ];
     platforms = platforms.unix;
   };
 }
-

pkgs/development/libraries/libxc/default.nix

@@ -1,13 +1,13 @@
 { stdenv, fetchurl, gfortran, perl }:
 
 let
-  version = "3.0.1";
+  version = "4.2.3";
 
 in stdenv.mkDerivation {
   name = "libxc-${version}";
   src = fetchurl {
     url = "http://www.tddft.org/programs/octopus/down.php?file=libxc/${version}/libxc-${version}.tar.gz";
-    sha256 = "1xyac89yx03vm86rvk07ps1d39xss3amw46a1k53mv30mgr94rl3";
+    sha256 = "0mj26jga0nj76blf2rp9cmgf0v0yhsp7xrg92zgih7fjlydrxr02";
   };
 
   buildInputs = [ gfortran ];

pkgs/development/libraries/mlt/default.nix

@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   name = "mlt-${version}";
-  version = "6.8.0";
+  version = "6.10.0";
 
   src = fetchFromGitHub {
     owner = "mltframework";
     repo = "mlt";
     rev = "v${version}";
-    sha256 = "0hmxlz3i9yasw5jdkrczak8shzlnpi1acaahn50lvgg9b14kg7b8";
+    sha256 = "0ki86yslr5ywa6sz8pjrgd9a4rn2rr4mss2zkmqi7pq8prgsm1fr";
   };
 
   buildInputs = [

pkgs/development/ocaml-modules/lwt/default.nix

@@ -1,6 +1,8 @@
 { stdenv, fetchzip, pkgconfig, ncurses, libev, jbuilder
-, ocaml, findlib, camlp4, cppo
+, ocaml, findlib, cppo
 , ocaml-migrate-parsetree, ppx_tools_versioned, result
+, withP4 ? !stdenv.lib.versionAtLeast ocaml.version "4.07"
+, camlp4 ? null
 }:
 
 stdenv.mkDerivation rec {
@@ -13,12 +15,13 @@ stdenv.mkDerivation rec {
   };
 
   preConfigure = ''
-    ocaml src/util/configure.ml -use-libev true -use-camlp4 true
+    ocaml src/util/configure.ml -use-libev true -use-camlp4 ${if withP4 then "true" else "false"}
   '';
 
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ ncurses ocaml findlib jbuilder camlp4 cppo
+  buildInputs = [ ncurses ocaml findlib jbuilder cppo
-    ocaml-migrate-parsetree ppx_tools_versioned ];
+    ocaml-migrate-parsetree ppx_tools_versioned ]
+  ++ stdenv.lib.optional withP4 camlp4;
   propagatedBuildInputs = [ libev result ];
 
   installPhase = ''

pkgs/development/ocaml-modules/lwt_log/default.nix

@@ -0,0 +1,24 @@
+{ stdenv, ocaml, findlib, jbuilder, lwt }:
+
+stdenv.mkDerivation rec {
+  version = "1.0.0";
+  name = "ocaml${ocaml.version}-lwt_log-${version}";
+
+  inherit (lwt) src;
+
+  buildInputs = [ ocaml findlib jbuilder ];
+
+  propagatedBuildInputs = [ lwt ];
+
+  buildPhase = "jbuilder build -p lwt_log";
+
+  inherit (jbuilder) installPhase;
+
+  meta = {
+    description = "Lwt logging library (deprecated)";
+    homepage = "https://github.com/aantron/lwt_log";
+    license = stdenv.lib.licenses.lgpl21;
+    inherit (ocaml.meta) platforms;
+    maintainers = [ stdenv.lib.maintainers.vbgl ];
+  };
+}

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

@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, iana-etc, libredirect,
+{ stdenv, buildPythonPackage, fetchPypi, fetchpatch, iana-etc, libredirect,
   pytest, case, kombu, billiard, pytz, anyjson, amqp, eventlet
 }:
 
@@ -11,6 +11,13 @@ buildPythonPackage rec {
     sha256 = "ff727c115533edbc7b81b2b4ba1ec88d1c2fc4836e1e2f4c3c33a76ff53e5d7f";
   };
 
+  # Skip test_RedisBackend.test_timeouts_in_url_coerced
+  # See https://github.com/celery/celery/pull/4847
+  patches = fetchpatch {
+    url = https://github.com/celery/celery/commit/b2668607c909c61becd151905b4525190c19ff4a.patch;
+    sha256 = "11w0z2ycyh8kccj4y69zb7bxppiipcwwigg6jn1q9yrcsvz170jq";
+  };
+
   # make /etc/protocols accessible to fix socket.getprotobyname('tcp') in sandbox
   preCheck = stdenv.lib.optionalString stdenv.isLinux ''
     export NIX_REDIRECTS=/etc/protocols=${iana-etc}/etc/protocols \

pkgs/development/python-modules/cmd2/default.nix

@@ -1,17 +1,15 @@
-{ stdenv, fetchPypi, buildPythonPackage, pythonOlder
+{ stdenv, fetchPypi, buildPythonPackage, pythonOlder, isPy3k
-, pyperclip, six, pyparsing, vim
+, pyperclip, six, pyparsing, vim, wcwidth, colorama
 , contextlib2 ? null, subprocess32 ? null
 , pytest, mock, which, fetchFromGitHub, glibcLocales
 }:
 buildPythonPackage rec {
   pname = "cmd2";
-  version = "0.8.0";
+  version = "0.9.1";
 
-  src = fetchFromGitHub {
+  src = fetchPypi {
-    owner = "python-cmd2";
+    inherit pname version;
-    repo = "cmd2";
+    sha256 = "1wpw4f9zix30hfncm0hwxjjdx78zq26x3r8s9nvsq9vnxf41xb49";
-    rev = version;
-    sha256 = "0nw2b7n7zg51bc3glxw0l9fn91mwjnjshklhmxhyvjbsg7khf64z";
   };
 
   LC_ALL="en_US.UTF-8";
@@ -31,14 +29,16 @@ buildPythonPackage rec {
     py.test -k 'not test_path_completion_user_expansion'
   '';
   doCheck = !stdenv.isDarwin;
+  disabled = !isPy3k;
 
   propagatedBuildInputs = [
+    colorama
     pyperclip
     six
     pyparsing
+    wcwidth
   ]
   ++ stdenv.lib.optional (pythonOlder "3.5") contextlib2
-  ++ stdenv.lib.optional (pythonOlder "3.0") subprocess32
   ;
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/cmd2/old.nix

@@ -0,0 +1,49 @@
+{ stdenv, fetchPypi, buildPythonPackage, pythonOlder
+, pyperclip, six, pyparsing, vim
+, contextlib2 ? null, subprocess32 ? null
+, pytest, mock, which, fetchFromGitHub, glibcLocales
+}:
+buildPythonPackage rec {
+  pname = "cmd2";
+  version = "0.8.0";
+
+  src = fetchFromGitHub {
+    owner = "python-cmd2";
+    repo = "cmd2";
+    rev = version;
+    sha256 = "0nw2b7n7zg51bc3glxw0l9fn91mwjnjshklhmxhyvjbsg7khf64z";
+  };
+
+  LC_ALL="en_US.UTF-8";
+
+  postPatch = stdenv.lib.optional stdenv.isDarwin ''
+    # Fake the impure dependencies pbpaste and pbcopy
+    mkdir bin
+    echo '#/bin/sh' > bin/pbpaste
+    echo '#/bin/sh' > bin/pbcopy
+    chmod +x bin/{pbcopy,pbpaste}
+    export PATH=$(realpath bin):$PATH
+  '';
+
+  checkInputs= [ pytest mock which vim glibcLocales ];
+  checkPhase = ''
+    # test_path_completion_user_expansion might be fixed in the next release
+    py.test -k 'not test_path_completion_user_expansion'
+  '';
+  doCheck = !stdenv.isDarwin;
+
+  propagatedBuildInputs = [
+    pyperclip
+    six
+    pyparsing
+  ]
+  ++ stdenv.lib.optional (pythonOlder "3.5") contextlib2
+  ++ stdenv.lib.optional (pythonOlder "3.0") subprocess32
+  ;
+
+  meta = with stdenv.lib; {
+    description = "Enhancements for standard library's cmd module";
+    homepage = https://github.com/python-cmd2/cmd2;
+    maintainers = with maintainers; [ teto ];
+  };
+}

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

@@ -46,6 +46,11 @@ buildPythonPackage rec {
     export CVXOPT_FFTW_INC_DIR=${fftw.dev}/include
   '';
 
+  # https://github.com/cvxopt/cvxopt/issues/122
+  # This is fixed on staging (by #43234, status 2018-07-15), but until that
+  # lands we should disable the tests. Otherwise the 99% of use cases that
+  # should be unaffected by that failure are affected.
+  doCheck = false;
   checkPhase = ''
     ${python.interpreter} -m unittest discover -s tests
   '';

pkgs/development/python-modules/cypari2/default.nix

@@ -7,16 +7,15 @@
 , gmp
 , cython
 , cysignals
-, six
 }:
 
 buildPythonPackage rec {
   pname = "cypari2";
-  version = "1.1.4"; # remove six dependency on upgrade to >1.1.4
+  version = "1.2.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0n0mp8qmvvzmfaawg39d3mkyzf65q2zkz7bnqyk4sfjbz4xwc6mb";
+    sha256 = "0v2kikwf0advq8j76nwzhlacwj1yys9cvajm4fqgmasjdsnf1q4k";
   };
 
   # This differs slightly from the default python installPhase in that it pip-installs
@@ -39,7 +38,6 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     cysignals
     cython
-    six # after 1.1.4: will not be needed
   ];
 
   checkPhase = ''

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

@@ -1,5 +1,6 @@
-{ lib, buildPythonPackage, fetchPypi,
+{ lib, buildPythonPackage, fetchPypi
-  celery, django, psycopg2
+, glibcLocales
+, celery, django, psycopg2
 }:
 
 buildPythonPackage rec {
@@ -7,7 +8,7 @@ buildPythonPackage rec {
   version = "1.1.0";
 
   meta = {
-    description = "Simple, powerfull and nonobstructive django email middleware.";
+    description = "Simple, powerfull and nonobstructive django email middleware";
     homepage = https://github.com/bameda/djmail;
     license = lib.licenses.bsd3;
   };
@@ -17,6 +18,10 @@ buildPythonPackage rec {
     sha256 = "87d2a8b4bdf67ae9b312e127ccc873a53116cf297ec786460d782ce82eaa76b5";
   };
 
+  nativeBuildInputs = [ glibcLocales ];
+
+  LC_ALL = "en_US.UTF-8";
+
   propagatedBuildInputs = [ celery django psycopg2 ];
 
   # django.core.exceptions.ImproperlyConfigured: Requested setting DEFAULT_INDEX_TABLESPACE, but settings are not configured. You must either define the environment variable DJANGO_SETTINGS_MODULE or call settings.configure() before accessing settings.

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

@@ -4,17 +4,12 @@
 buildPythonPackage rec {
   pname = "Eve";
   version = "0.8";
-  name  = "${pname}-${version}";
 
   src = fetchPypi {
     inherit pname version;
     sha256 = "9f926c715f88c7a92dc2b950ccc09cccd91f72fe0e93cde806b85d25b947df2f";
   };
 
-  patches = [
-    ./setup.patch
-  ];
-
   propagatedBuildInputs = [
     cerberus
     events

pkgs/development/python-modules/eve/setup.patch

@@ -1,21 +0,0 @@
-diff --git i/setup.py w/setup.py
-index 0176467..2b74988 100755
---- i/setup.py
-+++ w/setup.py
-@@ -9,11 +9,11 @@ install_requires = [
-     'cerberus>=0.9.2,<0.10',
-     'events>=0.2.1,<0.3',
-     'simplejson>=3.3.0,<4.0',
--    'werkzeug>=0.9.4,<=0.11.15',
--    'markupsafe>=0.23,<1.0',
--    'jinja2>=2.8,<3.0',
--    'itsdangerous>=0.24,<1.0',
--    'flask>=0.10.1,<=0.12',
-+    'werkzeug>=0.9.4',
-+    'markupsafe>=0.23',
-+    'jinja2>=2.8',
-+    'itsdangerous>=0.24',
-+    'flask>=0.10.1',
-     'pymongo>=3.4',
-     'flask-pymongo>=0.4',
- ]

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

@@ -0,0 +1,17 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "Events";
+  version = "0.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "f4d9c41a5c160ce504278f219fe56f44242ca63794a0ad638b52d1e087ac2a41";
+  };
+
+  meta = with lib; {
+    homepage = http://events.readthedocs.org;
+    description = "Bringing the elegance of C# EventHanlder to Python";
+    license = licenses.bsd3;
+  };
+}

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

@@ -0,0 +1,25 @@
+{ lib, buildPythonPackage, fetchPypi, pytest, case, pytz, amqp }:
+
+buildPythonPackage rec {
+    pname = "kombu";
+    version = "4.2.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "86adec6c60f63124e2082ea8481bbe4ebe04fde8ebed32c177c7f0cd2c1c9082";
+  };
+
+  postPatch = ''
+    substituteInPlace requirements/test.txt --replace "pytest-sugar" ""
+  '';
+
+  checkInputs = [ pytest case pytz ];
+
+  propagatedBuildInputs = [ amqp ];
+
+  meta = with lib; {
+    description = "Messaging library for Python";
+    homepage    = https://github.com/celery/kombu;
+    license     = licenses.bsd3;
+  };
+}

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

@@ -14,6 +14,10 @@ buildPythonPackage rec {
     sha256 = "5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0";
   };
 
+  # basically https://github.com/scikit-learn/scikit-learn/pull/10723,
+  # but rebased onto 0.19.1
+  patches = [ ./n_iter-should-be-less-than-max_iter-using-lbgfs.patch ];
+
   buildInputs = [ nose pillow gfortran glibcLocales ];
   propagatedBuildInputs = [ numpy scipy numpy.blas ];
 

pkgs/development/python-modules/scikitlearn/n_iter-should-be-less-than-max_iter-using-lbgfs.patch

@@ -0,0 +1,73 @@
+diff --git a/sklearn/linear_model/huber.py b/sklearn/linear_model/huber.py
+index e17dc1e..665654d 100644
+--- a/sklearn/linear_model/huber.py
++++ b/sklearn/linear_model/huber.py
+@@ -181,7 +181,11 @@ class HuberRegressor(LinearModel, RegressorMixin, BaseEstimator):
+ 
+     n_iter_ : int
+         Number of iterations that fmin_l_bfgs_b has run for.
+-        Not available if SciPy version is 0.9 and below.
++
++        .. versionchanged:: 0.20
++
++            In SciPy <= 1.0.0 the number of lbfgs iterations may exceed
++            ``max_iter``. ``n_iter_`` will now report at most ``max_iter``.
+ 
+     outliers_ : array, shape (n_samples,)
+         A boolean mask which is set to True where the samples are identified
+@@ -272,7 +276,9 @@ class HuberRegressor(LinearModel, RegressorMixin, BaseEstimator):
+             raise ValueError("HuberRegressor convergence failed:"
+                              " l-BFGS-b solver terminated with %s"
+                              % dict_['task'].decode('ascii'))
+-        self.n_iter_ = dict_.get('nit', None)
++        # In scipy <= 1.0.0, nit may exceed maxiter.
++        # See https://github.com/scipy/scipy/issues/7854.
++        self.n_iter_ = min(dict_.get('nit', None), self.max_iter)
+         self.scale_ = parameters[-1]
+         if self.fit_intercept:
+             self.intercept_ = parameters[-2]
+diff --git a/sklearn/linear_model/logistic.py b/sklearn/linear_model/logistic.py
+index 8646c9a..c72a7d9 100644
+--- a/sklearn/linear_model/logistic.py
++++ b/sklearn/linear_model/logistic.py
+@@ -718,7 +718,9 @@ def logistic_regression_path(X, y, pos_class=None, Cs=10, fit_intercept=True,
+                 warnings.warn("lbfgs failed to converge. Increase the number "
+                               "of iterations.")
+             try:
+-                n_iter_i = info['nit'] - 1
++                # In scipy <= 1.0.0, nit may exceed maxiter.
++                # See https://github.com/scipy/scipy/issues/7854.
++                n_iter_i = min(info['nit'], max_iter)
+             except:
+                 n_iter_i = info['funcalls'] - 1
+         elif solver == 'newton-cg':
+@@ -1115,6 +1117,11 @@ class LogisticRegression(BaseEstimator, LinearClassifierMixin,
+         it returns only 1 element. For liblinear solver, only the maximum
+         number of iteration across all classes is given.
+ 
++        .. versionchanged:: 0.20
++
++            In SciPy <= 1.0.0 the number of lbfgs iterations may exceed
++            ``max_iter``. ``n_iter_`` will now report at most ``max_iter``.
++
+     See also
+     --------
+     SGDClassifier : incrementally trained logistic regression (when given
+diff --git a/sklearn/linear_model/tests/test_huber.py b/sklearn/linear_model/tests/test_huber.py
+index 08f4fdf..ca1092f 100644
+--- a/sklearn/linear_model/tests/test_huber.py
++++ b/sklearn/linear_model/tests/test_huber.py
+@@ -42,6 +42,13 @@ def test_huber_equals_lr_for_high_epsilon():
+     assert_almost_equal(huber.intercept_, lr.intercept_, 2)
+ 
+ 
++def test_huber_max_iter():
++    X, y = make_regression_with_outliers()
++    huber = HuberRegressor(max_iter=1)
++    huber.fit(X, y)
++    assert huber.n_iter_ == huber.max_iter
++
++
+ def test_huber_gradient():
+     # Test that the gradient calculated by _huber_loss_and_gradient is correct
+     rng = np.random.RandomState(1)

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

@@ -0,0 +1,26 @@
+{ stdenv, fetchurl, buildPythonPackage }:
+
+buildPythonPackage rec {
+    name = "wcwidth-${version}";
+    version = "0.1.7";
+
+    src = fetchurl {
+      url = "mirror://pypi/w/wcwidth/${name}.tar.gz";
+      sha256 = "0pn6dflzm609m4r3i8ik5ni9ijjbb5fa3vg1n7hn6vkd49r77wrx";
+    };
+
+    # Checks fail due to missing tox.ini file:
+    doCheck = false;
+
+    meta = with stdenv.lib; {
+      description = "Measures number of Terminal column cells of wide-character codes";
+      longDescription = ''
+        This API is mainly for Terminal Emulator implementors -- any Python
+        program that attempts to determine the printable width of a string on
+        a Terminal. It is implemented in python (no C library calls) and has
+        no 3rd-party dependencies.
+      '';
+      homepage = https://github.com/jquast/wcwidth;
+      license = licenses.mit;
+    };
+  }

pkgs/development/tools/analysis/flow/default.nix

@@ -1,5 +1,4 @@
-{ stdenv, fetchFromGitHub, lib, ocaml, libelf, cf-private, CoreServices,
+{ stdenv, fetchFromGitHub, lib, ocamlPackages, libelf, cf-private, CoreServices }:
-  findlib, camlp4, sedlex, ocamlbuild, lwt_ppx, wtf8, dtoa }:
 
 with lib;
 
@@ -14,21 +13,15 @@ stdenv.mkDerivation rec {
     sha256 = "0r3yl4m7dhm1h4c431zp8hd2gg6k1d9bwd2371xav5q7hviwmjl6";
   };
 
-  # lwt.log is being split out into a separate package, so this can be
-  # removed once nixpkgs is updated.
-  # See https://github.com/ocsigen/lwt/issues/453#issuecomment-352897664
-  postPatch = ''
-    substituteInPlace Makefile --replace lwt_log lwt.log
-  '';
-
   installPhase = ''
     mkdir -p $out/bin
     cp bin/flow $out/bin/
   '';
 
-  buildInputs = [
+  buildInputs = [ libelf
-    ocaml libelf findlib camlp4 sedlex ocamlbuild lwt_ppx wtf8 dtoa
+  ] ++ (with ocamlPackages; [
-  ] ++ optionals stdenv.isDarwin [ cf-private CoreServices ];
+    ocaml findlib camlp4 sedlex ocamlbuild lwt_ppx lwt_log wtf8 dtoa
+  ]) ++ optionals stdenv.isDarwin [ cf-private CoreServices ];
 
   meta = with stdenv.lib; {
     description = "A static type checker for JavaScript";

pkgs/development/tools/bloaty/default.nix

@@ -1,14 +1,14 @@
 { stdenv, binutils, cmake, zlib, fetchFromGitHub }:
 
 stdenv.mkDerivation rec {
-  version = "2018-05-22";
+  version = "2018-06-15";
   name = "bloaty-${version}";
 
   src = fetchFromGitHub {
     owner = "google";
     repo = "bloaty";
-    rev = "054788b091ccfd43b05b9817062139145096d440";
+    rev = "bdbb3ce196c86d2154f5fba99b5ff73ca43446a9";
-    sha256 = "0pmv66137ipzsjjdz004n61pz3aipjhh3b0w0y1406clqpwkvpjm";
+    sha256 = "1r7di2p8bi12jpgl6cm4ygi1s0chv767mdcavc7pb45874vl02fx";
     fetchSubmodules = true;
   };
 
@@ -20,8 +20,6 @@ stdenv.mkDerivation rec {
 
   doCheck = true;
 
-  checkPhase = "ctest";
-
   installPhase = ''
     install -Dm755 {.,$out/bin}/bloaty
   '';

pkgs/development/tools/build-managers/cask/default.nix

@@ -1,11 +0,0 @@
-{ emacsPackagesNg, writeScriptBin }:
-let
-
-  emacs = emacsPackagesNg.emacsWithPackages (epkgs: [ epkgs.cask-package-toolset ]);
-  cpt = emacsPackagesNg.cask-package-toolset;
-
-in writeScriptBin "cask" ''
-#!/bin/sh
-
-exec ${emacs}/bin/emacs --script ${cpt}/share/emacs/site-lisp/elpa/cask-package-toolset-${cpt.version}/cask-package-toolset.el -- "$@"
-''

pkgs/development/tools/build-managers/rebar3/default.nix

@@ -3,19 +3,19 @@
   tree, fetchFromGitHub, hexRegistrySnapshot }:
 
 let
-  version = "3.4.3";
+  version = "3.6.1";
 
   bootstrapper = ./rebar3-nix-bootstrap;
 
   erlware_commons = fetchHex {
     pkg = "erlware_commons";
-    version = "1.0.0";
+    version = "1.2.0";
-    sha256 = "0wkphbrjk19lxdwndy92v058qwcaz13bcgdzp33h21aa7vminzx7";
+    sha256 = "149kkn9gc9cjgvlmakygq475r63q2rry31s29ax0s425dh37sfl7";
   };
   ssl_verify_fun = fetchHex {
     pkg = "ssl_verify_fun";
-    version = "1.1.2";
+    version = "1.1.3";
-    sha256 = "0qdyx70v09fydv4wzz1djnkixqj62ny40yjjhv2q6mh47lns2arj";
+    sha256 = "1zljxashfhqmiscmf298vhr880ppwbgi2rl3nbnyvsfn0mjhw4if";
   };
   certifi = fetchHex {
     pkg = "certifi";
@@ -24,23 +24,23 @@ let
   };
   providers = fetchHex {
     pkg = "providers";
-    version = "1.6.0";
+    version = "1.7.0";
-    sha256 = "0byfa1h57n46jilz4q132j0vk3iqc0v1vip89li38gb1k997cs0g";
+    sha256 = "19p4rbsdx9lm2ihgvlhxyld1q76kxpd7qwyqxxsgmhl5r8ln3rlb";
   };
   getopt = fetchHex {
     pkg = "getopt";
-    version = "0.8.2";
+    version = "1.0.1";
-    sha256 = "1xw30h59zbw957cyjd8n50hf9y09jnv9dyry6x3avfwzcyrnsvkk";
+    sha256 = "174mb46c2qd1f4a7507fng4vvscjh1ds7rykfab5rdnfp61spqak";
   };
   bbmustache = fetchHex {
     pkg = "bbmustache";
-    version = "1.3.0";
+    version = "1.5.0";
-    sha256 = "042pfgss8kscq6ssg8gix8ccmdsrx0anjczsbrn2a6c36ljrx2p6";
+    sha256 = "0xg3r4lxhqifrv32nm55b4zmkflacc1s964g15p6y6jfx6v4y1zd";
   };
   relx = fetchHex {
     pkg = "relx";
-    version = "3.23.1";
+    version = "3.26.0";
-    sha256 = "13j7wds2d7b8v3r9pwy3zhwhzywgwhn6l9gm3slqzyrs1jld0a9d";
+    sha256 = "1f810rb01kdidpa985s321ycg3y4hvqpzbk263n6i1bfnqykkvv9";
   };
   cf = fetchHex {
     pkg = "cf";
@@ -49,13 +49,13 @@ let
   };
   cth_readable = fetchHex {
     pkg = "cth_readable";
-    version = "1.3.0";
+    version = "1.4.2";
-    sha256 = "1s7bqj6f2zpbyjmbfq2mm6vcz1jrxjr2nd0531wshsx6fnshqhvs";
+    sha256 = "1pjid4f60pp81ds01rqa6ybksrnzqriw3aibilld1asn9iabxkav";
   };
   eunit_formatters = fetchHex {
     pkg = "eunit_formatters";
-    version = "0.3.1";
+    version = "0.5.0";
-    sha256 = "0cg9dasv60v09q3q4wja76pld0546mhmlpb0khagyylv890hg934";
+    sha256 = "1jb3hzb216r29x2h4pcjwfmx1k81431rgh5v0mp4x5146hhvmj6n";
   };
   rebar3_hex = fetchHex {
     pkg = "rebar3_hex";
@@ -70,7 +70,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url = "https://github.com/rebar/rebar3/archive/${version}.tar.gz";
-    sha256 = "1a05gpxxc3mx5v33kzpb5xnq5vglmjl0q8hrcvpinjlazcwbg531";
+    sha256 = "0cqhqymzh10pfyxqiy4hcg3d2myz3chx0y4m2ixmq8zk81acics0";
   };
 
   inherit bootstrapper;
@@ -121,6 +121,6 @@ stdenv.mkDerivation {
       '';
 
     platforms = stdenv.lib.platforms.unix;
-    maintainers = [ stdenv.lib.maintainers.gleber ];
+    maintainers = with stdenv.lib.maintainers; [ gleber tazjin ];
   };
 }

pkgs/development/tools/build-managers/rebar3/hermetic-rebar3.patch

@@ -1,5 +1,5 @@
 diff --git a/bootstrap b/bootstrap
-index 7c56bab..16c1be5 100755
+index 5dedd713..864056c4 100755
 --- a/bootstrap
 +++ b/bootstrap
 @@ -101,7 +101,7 @@ extract(Binary) ->
@@ -12,9 +12,8 @@ index 7c56bab..16c1be5 100755
                         [{body_format, binary}],
                         rebar) of
 diff --git a/src/rebar_hermeticity.erl b/src/rebar_hermeticity.erl
-new file mode 100644
+index e69de29b..8f6cc7d0 100644
-index 0000000..8f6cc7d
+--- a/src/rebar_hermeticity.erl
---- /dev/null
 +++ b/src/rebar_hermeticity.erl
 @@ -0,0 +1,42 @@
 +%% -*- erlang-indent-level: 4;indent-tabs-mode: nil -*-
@@ -60,20 +59,20 @@ index 0000000..8f6cc7d
 +    ?ERROR("Request: ~p ~s", [Method, Url]),
 +    erlang:halt(1).
 diff --git a/src/rebar_pkg_resource.erl b/src/rebar_pkg_resource.erl
-index d588f24..9ac8ad4 100644
+index 2cf167ee..6080aaca 100644
 --- a/src/rebar_pkg_resource.erl
 +++ b/src/rebar_pkg_resource.erl
-@@ -109,7 +109,7 @@ make_vsn(_) ->
+@@ -127,7 +127,7 @@ make_vsn(_) ->
  request(Url, ETag) ->
-     HttpOptions = [{ssl, ssl_opts(Url)}, {relaxed, true} | rebar_utils:get_proxy_auth()],
+     HttpOptions = [{ssl, ssl_opts(Url)},
- 
+                    {relaxed, true} | rebar_utils:get_proxy_auth()],
--    case httpc:request(get, {Url, [{"if-none-match", ETag} || ETag =/= false]++[{"User-Agent", rebar_utils:user_agent()}]},
+-    case httpc:request(get, {Url, [{"if-none-match", "\"" ++ ETag ++ "\""}
-+    case rebar_hermeticity:request(get, {Url, [{"if-none-match", ETag} || ETag =/= false]++[{"User-Agent", rebar_utils:user_agent()}]},
++    case rebar_hermeticity:request(get, {Url, [{"if-none-match", "\"" ++ ETag ++ "\""}
-                        HttpOptions,
+                                    || ETag =/= false] ++
-                        [{body_format, binary}],
+                              [{"User-Agent", rebar_utils:user_agent()}]},
-                        rebar) of
+                        HttpOptions, [{body_format, binary}], rebar) of
 diff --git a/src/rebar_prv_update.erl b/src/rebar_prv_update.erl
-index a019c5a..697cbab 100644
+index 17446311..4d44d794 100644
 --- a/src/rebar_prv_update.erl
 +++ b/src/rebar_prv_update.erl
 @@ -38,6 +38,8 @@ init(State) ->
@@ -85,17 +84,17 @@ index a019c5a..697cbab 100644
  do(State) ->
      try
          case rebar_packages:registry_dir(State) of
-@@ -52,7 +54,7 @@ do(State) ->
+@@ -53,7 +55,7 @@ do(State) ->
-                 case rebar_utils:url_append_path(CDN, ?REMOTE_REGISTRY_FILE) of
                      {ok, Url} ->
+                         HttpOptions = [{relaxed, true} | rebar_utils:get_proxy_auth()],
                          ?DEBUG("Fetching registry from ~p", [Url]),
 -                        case httpc:request(get, {Url, [{"User-Agent", rebar_utils:user_agent()}]},
 +                        case rebar_hermeticity:request(get, {Url, [{"User-Agent", rebar_utils:user_agent()}]},
-                                            [], [{stream, TmpFile}, {sync, true}],
+                                            HttpOptions, [{stream, TmpFile}, {sync, true}],
                                             rebar) of
                              {ok, saved_to_file} ->
-@@ -76,6 +78,7 @@ do(State) ->
+@@ -77,6 +79,7 @@ do(State) ->
-             ?DEBUG("Error creating package index: ~p ~p", [C, erlang:get_stacktrace()]),
+             ?DEBUG("Error creating package index: ~p ~p", [C, S]),
              throw(?PRV_ERROR(package_index_write))
      end.
 +-endif.

pkgs/development/tools/electron/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, libXScrnSaver, makeWrapper, fetchurl, unzip, atomEnv }:
+{ stdenv, lib, libXScrnSaver, makeWrapper, fetchurl, unzip, atomEnv, gtk2 }:
 
 let
   version = "1.8.2";
@@ -47,7 +47,7 @@ let
 
       patchelf \
         --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
-        --set-rpath "${atomEnv.libPath}:$out/lib/electron" \
+        --set-rpath "${atomEnv.libPath}:${gtk2}/lib:$out/lib/electron" \
         $out/lib/electron/electron
 
       wrapProgram $out/lib/electron/electron \

pkgs/development/tools/erlang/hex2nix/default.nix

@@ -1,32 +1,23 @@
-{ stdenv, fetchFromGitHub, buildRebar3, buildHex
+{ stdenv, fetchFromGitHub, buildRebar3, buildHex,
 
-, getopt_0_8_2, erlware_commons_1_0_0 }:
+  # Erlang dependencies:
+  ibrowse_4_2_2,
+  getopt_0_8_2,
+  erlware_commons_1_0_0,
+  jsx_2_8_0 }:
 
-let
-  ibrowse_4_4_0 = buildHex {
-    name = "ibrowse";
-    version = "4.4.0";
-    sha256 = "1hpic1xgksfm00mbl1kwmszca6jmjca32s7gdd8g11i0hy45k3ka";
-  };
-  jsx_2_8_2 = buildHex {
-    name = "jsx";
-    version = "2.8.2";
-    sha256 = "0k7lnmwqbgpmh90wy30kc0qlddkbh9r3sjlyayaqsz1r1cix7idl";
-  };
-
-in
 buildRebar3 rec {
     name = "hex2nix";
-    version = "0.0.6";
+    version = "0.0.6-a31eadd7";
 
     src = fetchFromGitHub {
-      owner = "erlang-nix";
+      owner  = "erlang-nix";
-      repo = "hex2nix";
+      repo   = "hex2nix";
-      rev = "${version}";
+      rev    = "a31eadd7af2cbdac1b87991b378e98ea4fb40ae0";
-      sha256 = "17rkzg836v7z2xf0i5m8zqfvr23dbmw1bi3c83km92f9glwa1dbf";
+      sha256 = "1hnkrksyrbpq2gq25rfsrnm86n0g3biab88gswm3zj88ddrz6dyk";
     };
 
-    beamDeps = [ ibrowse_4_4_0 jsx_2_8_2 erlware_commons_1_0_0 getopt_0_8_2 ];
+    beamDeps = [ ibrowse_4_2_2 jsx_2_8_0 erlware_commons_1_0_0 getopt_0_8_2 ];
 
     enableDebugInfo = true;
 

pkgs/development/tools/flyway/default.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, jre_headless, makeWrapper }:
   let
-    version = "5.1.3";
+    version = "5.1.4";
   in
     stdenv.mkDerivation {
       name = "flyway-${version}";
       src = fetchurl {
-        url = "https://repo1.maven.org/maven2/org/flywaydb/flyway-commandline/5.1.3/flyway-commandline-${version}.tar.gz";
+        url = "https://repo1.maven.org/maven2/org/flywaydb/flyway-commandline/5.1.4/flyway-commandline-${version}.tar.gz";
-        sha256 = "08nrjrpcb56f2mhghgjbvl7bfzvlgc81ykxzghq3kpslx5d560lm";
+        sha256 = "1raz125k55v6xa8gp6ylcjxz77r5364xqp9di46rayx3z2282f7q";
       };
       buildInputs = [ makeWrapper ];
       dontBuild = true;

pkgs/development/tools/misc/creduce/default.nix

@@ -8,18 +8,18 @@
 
 stdenv.mkDerivation rec {
   name = "creduce-${version}";
-  version = "2.7.0";
+  version = "2.8.0";
 
   src = fetchurl {
     url = "https://embed.cs.utah.edu/creduce/${name}.tar.gz";
-    sha256 = "0h8s4d54q6cl6i45x3143l2xmr29b2yhr3m0n5qqx63sr5csip1n";
+    sha256 = "1vqx73ymfscvlyig03972a5m7ar3gx2yv6m8c6h2mibz792j5xkp";
   };
 
+  nativeBuildInputs = [ cmake makeWrapper ];
   buildInputs = [
     # Ensure stdenv's CC is on PATH before clang-unwrapped
     stdenv.cc
     # Actual deps:
-    cmake makeWrapper
     llvm clang-unwrapped
     flex zlib
     perl ExporterLite FileWhich GetoptTabular RegexpCommon TermReadKey

pkgs/development/tools/misc/elfutils/default.nix

@@ -3,11 +3,11 @@
 # TODO: Look at the hardcoded paths to kernel, modules etc.
 stdenv.mkDerivation rec {
   name = "elfutils-${version}";
-  version = "0.172";
+  version = "0.173";
 
   src = fetchurl {
     url = "https://sourceware.org/elfutils/ftp/${version}/${name}.tar.bz2";
-    sha256 = "090fmbnvd9jblkwhb2bm3hanim63rrvd5f30mfxq4jac6kk9k73p";
+    sha256 = "1zq0l12k64hrbjmdjc4llrad96c25i427hpma1id9nk87w9qqvdp";
   };
 
   patches = ./debug-info-from-env.patch;

pkgs/development/tools/ocaml/jbuilder/default.nix

@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   name = "jbuilder-${version}";
-  version = "1.0+beta20";
+  version = "1.0.0";
   src = fetchFromGitHub {
     owner = "ocaml";
     repo = "dune";
     rev = "${version}";
-    sha256 = "0571lzm8caq6wnia7imgy4a27x5l2bvxiflg0jrwwml0ylnii65f";
+    sha256 = "08gb7l2rrfrsqvigna1cvvphww80zlvj7lqvaj4m4y9llanmnxcg";
   };
 
   buildInputs = with ocamlPackages; [ ocaml findlib ];
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
   preFixup = "rm -rf $out/jbuilder";
 
   meta = {
-    homepage = https://github.com/janestreet/jbuilder;
+    inherit (src.meta) homepage;
     description = "Fast, portable and opinionated build system";
     maintainers = [ stdenv.lib.maintainers.vbgl ];
     license = stdenv.lib.licenses.asl20;

pkgs/development/tools/vagrant/default.nix

@@ -1,9 +1,9 @@
 { lib, fetchurl, buildRubyGem, bundlerEnv, ruby, libarchive }:
 
 let
-  version = "2.1.1";
+  version = "2.1.2";
   url = "https://github.com/hashicorp/vagrant/archive/v${version}.tar.gz";
-  sha256 = "0kgsb33f3wh6x4450x74wri6z78ky92sfrv7ba7h7zmxsadb6m4b";
+  sha256 = "0fb90v43d30whhyjlgb9mmy93ccbpr01pz97kp5hrg3wfd7703b1";
 
   deps = bundlerEnv rec {
     name = "${pname}-${version}";

pkgs/games/dwarf-fortress/dfhack/default.nix

@@ -46,6 +46,7 @@ let
       fetchSubmodules = true;
     };
 
+    patches = [ ./fix-stonesense.patch ];
     nativeBuildInputs = [ cmake perl XMLLibXML XMLLibXSLT fakegit ];
     # We don't use system libraries because dfhack needs old C++ ABI.
     buildInputs = [ zlib SDL ]

pkgs/games/dwarf-fortress/dfhack/fix-stonesense.patch

@@ -0,0 +1,23 @@
+From f5be6fe5fb192f01ae4551ed9217e97fd7f6a0ae Mon Sep 17 00:00:00 2001
+From: Herwig Hochleitner <hhochleitner@gmail.com>
+Date: Sun, 1 Oct 2017 18:01:43 +0200
+Subject: [PATCH] include <GL/glext.h>
+
+this fixes `GLhandleARB` not being defined
+---
+ plugins/stonesense/common.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/plugins/stonesense/common.h b/plugins/stonesense/common.h
+index eb36691..ef45389 100644
+--- a/plugins/stonesense/common.h
++++ b/plugins/stonesense/common.h
+@@ -31,6 +31,8 @@ using namespace df::enums;
+ #include <allegro5/allegro_opengl.h>
+ #include <allegro5/utf8.h>
+ 
++#include <GL/glext.h>
++
+ // allegro leaks X headers, undef some of it here:
+ #undef TileShape
+ #undef None

pkgs/games/dwarf-fortress/dwarf-therapist/wrapper.nix

@@ -19,6 +19,7 @@ in symlinkJoin {
     # therefore uses many relative paths.
     wrapProgram $out/bin/dwarftherapist \
       --run "cd $out/share/dwarftherapist"
+    ln -s $out/bin/dwarftherapist $out/bin/DwarfTherapist
 
     rm -rf $out/share/dwarftherapist/memory_layouts/linux
     mkdir -p $out/share/dwarftherapist/memory_layouts/linux

pkgs/games/openrct2/default.nix

@@ -1,17 +1,24 @@
 { stdenv, fetchurl, fetchFromGitHub,
-  SDL2, cmake, curl, fontconfig, freetype, jansson, libiconv, libpng,
+  SDL2, cmake, curl, fontconfig, freetype, icu, jansson, libiconv, libpng,
   libpthreadstubs, libzip, libGLU, openssl, pkgconfig, speexdsp, zlib
 }:
 
 let
   name = "openrct2-${version}";
-  version = "0.1.2";
+  version = "0.2.0";
 
   openrct2-src = fetchFromGitHub {
     owner = "OpenRCT2";
     repo = "OpenRCT2";
     rev = "v${version}";
-    sha256 = "1zqrdxr79c9yx4bdxz1r5866hhwq0lcs9qpv3vhisr56ar5n5wk3";
+    sha256 = "1nmz8war8b49iicpc70gk7zlqizrvvwpidqm70lfpa0p68m7m3px";
+  };
+
+  objects-src = fetchFromGitHub {
+    owner = "OpenRCT2";
+    repo = "objects";
+    rev = "v1.0.2";
+    sha256 = "1gl37fmhhrfgd6gilw0n7hfdq80a9b31bi5r0xhxg7d579jccb04";
   };
 
   title-sequences-src = fetchFromGitHub {
@@ -32,6 +39,7 @@ stdenv.mkDerivation rec {
     curl
     fontconfig
     freetype
+    icu
     jansson
     libiconv
     libpng
@@ -45,11 +53,15 @@ stdenv.mkDerivation rec {
   ];
 
   postUnpack = ''
-    cp -r ${title-sequences-src} $sourceRoot/title
+    cp -r ${objects-src}         $sourceRoot/data/object
+    cp -r ${title-sequences-src} $sourceRoot/data/title
   '';
 
   cmakeFlags = [
-    "-DCMAKE_BUILD_TYPE=RELWITHDEBINFO" "-DDOWNLOAD_TITLE_SEQUENCES=OFF"];
+    "-DCMAKE_BUILD_TYPE=RELWITHDEBINFO"
+    "-DDOWNLOAD_OBJECTS=OFF"
+    "-DDOWNLOAD_TITLE_SEQUENCES=OFF"
+  ];
 
   makeFlags = ["all" "g2"];
 

pkgs/games/orthorobot/default.nix

@@ -1,8 +1,8 @@
-{ stdenv, fetchurl, unzip, love, lua, makeWrapper, makeDesktopItem }:
+{ stdenv, fetchurl, fetchFromGitHub, zip, love, lua, makeWrapper, makeDesktopItem }:
 
 let
   pname = "orthorobot";
-  version = "1.0";
+  version = "1.1.1";
 
   icon = fetchurl {
     url = "http://stabyourself.net/images/screenshots/orthorobot-5.png";
@@ -24,32 +24,26 @@ in
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
 
-  src = fetchurl {
+  src = fetchFromGitHub {
-    url = "http://stabyourself.net/dl.php?file=${pname}/${pname}-source.zip";
+    owner = "Stabyourself";
-    sha256 = "023nc3zwjkbmy4c8w6mfg39mg69zpqqr2gzlmp4fpydrjas70kbl";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1ca6hvd890kxmamsmsfiqzw15ngsvb4lkihjb6kabgmss61a6s5p";
   };
 
-  nativeBuildInputs = [ makeWrapper unzip ];
+  nativeBuildInputs = [ makeWrapper ];
-  buildInputs = [ lua love ];
+  buildInputs = [ lua love zip ];
 
   phases = [ "unpackPhase" "installPhase" ];
 
-  unpackPhase = ''
-    unzip -j $src
-  '';  
-
   installPhase =
   ''
-    mkdir -p $out/bin
+    mkdir -p $out/bin $out/share/games/lovegames $out/share/applications
-    mkdir -p $out/share/games/lovegames
+    zip -9 -r ${pname}.love ./*
-
+    mv ${pname}.love $out/share/games/lovegames/${pname}.love
-    cp -v ./*.love $out/share/games/lovegames/${pname}.love
-
     makeWrapper ${love}/bin/love $out/bin/${pname} --add-flags $out/share/games/lovegames/${pname}.love
-
-    chmod +x $out/bin/${pname}
-    mkdir -p $out/share/applications
     ln -s ${desktopItem}/share/applications/* $out/share/applications/
+    chmod +x $out/bin/${pname}
   '';
 
   meta = with stdenv.lib; {

pkgs/misc/themes/adapta/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "adapta-gtk-theme-${version}";
-  version = "3.93.1.28";
+  version = "3.94.0.1";
 
   src = fetchFromGitHub {
     owner = "adapta-project";
     repo = "adapta-gtk-theme";
     rev = version;
-    sha256 = "0r7fsyy074xd63p58fin3qsfq1535wafk0nag49551915hgdr18n";
+    sha256 = "17hck0hzkdj1bibn9wi7cxca8r539idb916v2l71gz7ynhav006d";
   };
 
   preferLocalBuild = true;

pkgs/os-specific/linux/bcc/default.nix

@@ -4,14 +4,14 @@
 }:
 
 python.pkgs.buildPythonApplication rec {
-  version = "0.5.0";
+  version = "0.6.0";
   name = "bcc-${version}";
 
   src = fetchFromGitHub {
-    owner = "iovisor";
+    owner  = "iovisor";
-    repo = "bcc";
+    repo   = "bcc";
-    rev = "v${version}";
+    rev    = "v${version}";
-    sha256 = "0bb3244xll5sqx0lvrchg71qy2zg0yj6r5h4v5fvrg1fjhaldys9";
+    sha256 = "1fk2kvbdvm87rkha2cigz2qhhlrni4g0dcnmiiyya79y85ahfvga";
   };
 
   format = "other";
@@ -23,12 +23,6 @@ python.pkgs.buildPythonApplication rec {
   ];
 
   patches = [
-    # fix build with llvm > 5.0.0 && < 6.0.0
-    (fetchpatch {
-      url = "https://github.com/iovisor/bcc/commit/bd7fa55bb39b8978dafd0b299e35616061e0a368.patch";
-      sha256 = "1sgxhsq174iihyk1x08py73q8fh78d7y3c90k5nh8vcw2pf1xbnf";
-    })
-
     # This is needed until we fix
     # https://github.com/NixOS/nixpkgs/issues/40427
     ./fix-deadlock-detector-import.patch

pkgs/servers/sql/postgresql/timescaledb/default.nix

@@ -8,7 +8,7 @@
 
 stdenv.mkDerivation rec {
   name = "timescaledb-${version}";
-  version = "0.9.2";
+  version = "0.10.1";
 
   nativeBuildInputs = [ cmake ];
   buildInputs = [ postgresql ];
@@ -17,7 +17,7 @@ stdenv.mkDerivation rec {
     owner  = "timescale";
     repo   = "timescaledb";
     rev    = "refs/tags/${version}";
-    sha256 = "1zgyd407skqbsw2zj3l9hixwlisnj82yb6hbq5khjg9k0ifvvgyp";
+    sha256 = "07qkkf7lbwaig26iia54vdakwmv33f71p8saqifz9lf0zy6xn0w0";
   };
 
   # Fix the install phase which tries to install into the pgsql extension dir,
@@ -34,6 +34,13 @@ stdenv.mkDerivation rec {
     done
   '';
 
+  postInstall = ''
+    # work around an annoying bug, by creating $out/bin, so buildEnv doesn't freak out later
+    # see https://github.com/NixOS/nixpkgs/issues/22653
+
+    mkdir -p $out/bin
+  '';
+
   meta = with stdenv.lib; {
     description = "Scales PostgreSQL for time-series data via automatic partitioning across time and space";
     homepage    = https://www.timescale.com/;