merge: fixing changes with nixpkgs since pull-request

- pytest-timeout: no longer requires patch - joblib: was improperly merged with the github merge tool (never using again)
2018-09-10 23:09:00 -04:00 · 2018-09-10 23:09:00 -04:00 · dac171dd5d
commit dac171dd5d
parent ed130935c8 8ebb27d4a6
411 changed files with 14656 additions and 8216 deletions
--- a/doc/cross-compilation.xml
+++ b/doc/cross-compilation.xml
@ -47,13 +47,9 @@

   <para>
    In Nixpkgs, these three platforms are defined as attribute sets under the
-    names <literal>buildPlatform</literal>, <literal>hostPlatform</literal>,
-    and <literal>targetPlatform</literal>. All three are always defined as
-    attributes in the standard environment, and at the top level. That means
-    one can get at them just like a dependency in a function that is imported
-    with <literal>callPackage</literal>:
-<programlisting>{ stdenv, buildPlatform, hostPlatform, fooDep, barDep, .. }: ...buildPlatform...</programlisting>
-    , or just off <varname>stdenv</varname>:
+    names <literal>buildPlatform</literal>, <literal>hostPlatform</literal>, and
+    <literal>targetPlatform</literal>. They are always defined as attributes in
+    the standard environment. That means one can access them like:
 <programlisting>{ stdenv, fooDep, barDep, .. }: ...stdenv.buildPlatform...</programlisting>
    .
   </para>
--- a/doc/languages-frameworks/vim.section.md
+++ b/doc/languages-frameworks/vim.section.md
@ -5,11 +5,16 @@ date: 2016-06-25
 ---
 # User's Guide to Vim Plugins/Addons/Bundles/Scripts in Nixpkgs

-You'll get a vim(-your-suffix) in PATH also loading the plugins you want.
+Both Neovim and Vim can be configured to include your favorite plugins
+and additional libraries.
+
 Loading can be deferred; see examples.

-Vim packages, VAM (=vim-addon-manager) and Pathogen are supported to load
-packages.
+At the moment we support three different methods for managing plugins:
+
+- Vim packages (*recommend*)
+- VAM (=vim-addon-manager)
+- Pathogen

 ## Custom configuration

@ -25,7 +30,19 @@ vim_configurable.customize {
 }
 ```

-## Vim packages
+For Neovim the `configure` argument can be overridden to achieve the same:
+
+```
+neovim.override {
+  configure = {
+    customRC = ''
+      # here your custom configuration goes!
+    '';
+  };
+}
+```
+
+## Managing plugins with Vim packages

 To store you plugins in Vim packages the following example can be used:

@ -38,13 +55,50 @@ vim_configurable.customize {
    opt = [ phpCompletion elm-vim ];
    # To automatically load a plugin when opening a filetype, add vimrc lines like:
    # autocmd FileType php :packadd phpCompletion
-  }
-};
+  };
+}
 ```

-## VAM
+For Neovim the syntax is

-### dependencies by Vim plugins
+```
+neovim.override {
+  configure = {
+    customRC = ''
+      # here your custom configuration goes!
+    '';
+    packages.myVimPackage = with pkgs.vimPlugins; {
+      # see examples below how to use custom packages
+      start = [ ];
+      opt = [ ];
+    };
+  };
+}
+```
+
+The resulting package can be added to `packageOverrides` in `~/.nixpkgs/config.nix` to make it installable:
+
+```
+{
+  packageOverrides = pkgs: with pkgs; {
+    myVim = vim_configurable.customize {
+      name = "vim-with-plugins";
+      # add here code from the example section
+    };
+    myNeovim = neovim.override {
+      configure = {
+      # add here code from the example section
+      };
+    };
+  };
+}
+```
+
+After that you can install your special grafted `myVim` or `myNeovim` packages.
+
+## Managing plugins with VAM
+
+### Handling dependencies of Vim plugins

 VAM introduced .json files supporting dependencies without versioning
 assuming that "using latest version" is ok most of the time.
@ -125,6 +179,18 @@ Sample output2:
    ]


+## Adding new plugins to nixpkgs
+
+In `pkgs/misc/vim-plugins/vim-plugin-names` we store the plugin names
+for all vim plugins we automatically generate plugins for.
+The format of this file `github username/github repository`:
+For example https://github.com/scrooloose/nerdtree becomes `scrooloose/nerdtree`.
+After adding your plugin to this file run the `./update.py` in the same folder.
+This will updated a file called `generated.nix` and make your plugin accessible in the
+`vimPlugins` attribute set (`vimPlugins.nerdtree` in our example).
+If additional steps to the build process of the plugin are required, add an
+override to the `pkgs/misc/vim-plugins/default.nix` in the same directory.
+
 ## Important repositories

 - [vim-pi](https://bitbucket.org/vimcommunity/vim-pi) is a plugin repository
--- a/doc/package-notes.xml
+++ b/doc/package-notes.xml
@ -671,6 +671,8 @@ overrides = super: self: rec {
    plugins = with availablePlugins; [ python perl ];
  }
 }</programlisting>
+    If the <literal>configure</literal> function returns an attrset without the <literal>plugins</literal>
+    attribute, <literal>availablePlugins</literal> will be used automatically.
  </para>

  <para>
@ -704,6 +706,55 @@ overrides = super: self: rec {
 }; }
 </programlisting>
  </para>
+  <para>
+    WeeChat allows to set defaults on startup using the <literal>--run-command</literal>.
+    The <literal>configure</literal> method can be used to pass commands to the program:
+<programlisting>weechat.override {
+  configure = { availablePlugins, ... }: {
+    init = ''
+      /set foo bar
+      /server add freenode chat.freenode.org
+    '';
+  };
+}</programlisting>
+    Further values can be added to the list of commands when running
+    <literal>weechat --run-command "your-commands"</literal>.
+  </para>
+  <para>
+    Additionally it's possible to specify scripts to be loaded when starting <literal>weechat</literal>.
+    These will be loaded before the commands from <literal>init</literal>:
+<programlisting>weechat.override {
+  configure = { availablePlugins, ... }: {
+    scripts = with pkgs.weechatScripts; [
+      weechat-xmpp weechat-matrix-bridge wee-slack
+    ];
+    init = ''
+      /set plugins.var.python.jabber.key "val"
+    '':
+  };
+}</programlisting>
+  </para>
+  <para>
+    In <literal>nixpkgs</literal> there's a subpackage which contains derivations for
+    WeeChat scripts. Such derivations expect a <literal>passthru.scripts</literal> attribute
+    which contains a list of all scripts inside the store path. Furthermore all scripts
+    have to live in <literal>$out/share</literal>. An exemplary derivation looks like this:
+<programlisting>{ stdenv, fetchurl }:
+
+stdenv.mkDerivation {
+  name = "exemplary-weechat-script";
+  src = fetchurl {
+    url = "https://scripts.tld/your-scripts.tar.gz";
+    sha256 = "...";
+  };
+  passthru.scripts = [ "foo.py" "bar.lua" ];
+  installPhase = ''
+    mkdir $out/share
+    cp foo.py $out/share
+    cp bar.lua $out/share
+  '';
+}</programlisting>
+  </para>
 </section>
 <section xml:id="sec-citrix">
  <title>Citrix Receiver</title>
--- a/lib/asserts.nix
+++ b/lib/asserts.nix
@ -0,0 +1,44 @@
+{ lib }:
+
+rec {
+
+  /* Print a trace message if pred is false.
+     Intended to be used to augment asserts with helpful error messages.
+
+     Example:
+       assertMsg false "nope"
+       => false
+       stderr> trace: nope
+
+       assert (assertMsg ("foo" == "bar") "foo is not bar, silly"); ""
+       stderr> trace: foo is not bar, silly
+       stderr> assert failed at …
+
+     Type:
+       assertMsg :: Bool -> String -> Bool
+  */
+  # TODO(Profpatsch): add tests that check stderr
+  assertMsg = pred: msg:
+    if pred
+    then true
+    else builtins.trace msg false;
+
+  /* Specialized `assertMsg` for checking if val is one of the elements
+     of a list. Useful for checking enums.
+
+     Example:
+       let sslLibrary = "libressl"
+       in assertOneOf "sslLibrary" sslLibrary [ "openssl" "bearssl" ]
+       => false
+       stderr> trace: sslLibrary must be one of "openssl", "bearssl", but is: "libressl"
+
+     Type:
+       assertOneOf :: String -> ComparableVal -> List ComparableVal -> Bool
+  */
+  assertOneOf = name: val: xs: assertMsg
+    (lib.elem val xs)
+    "${name} must be one of ${
+      lib.generators.toPretty {} xs}, but is: ${
+        lib.generators.toPretty {} val}";
+
+}
--- a/lib/default.nix
+++ b/lib/default.nix
@ -38,10 +38,11 @@ let
    systems = callLibs ./systems;

    # misc
+    asserts = callLibs ./asserts.nix;
    debug = callLibs ./debug.nix;
-
    generators = callLibs ./generators.nix;
    misc = callLibs ./deprecated.nix;
+
    # domain-specific
    fetchers = callLibs ./fetchers.nix;

@ -60,7 +61,6 @@ let
      boolToString mergeAttrs flip mapNullable inNixShell min max
      importJSON warn info nixpkgsVersion version mod compare
      splitByAndCompare functionArgs setFunctionArgs isFunction;
-
    inherit (fixedPoints) fix fix' extends composeExtensions
      makeExtensible makeExtensibleWithCustomName;
    inherit (attrsets) attrByPath hasAttrByPath setAttrByPath
@ -117,6 +117,8 @@ let
      unknownModule mkOption;
    inherit (types) isType setType defaultTypeMerge defaultFunctor
      isOptionType mkOptionType;
+    inherit (asserts)
+      assertMsg assertOneOf;
    inherit (debug) addErrorContextToAttrs traceIf traceVal traceValFn
      traceXMLVal traceXMLValMarked traceSeq traceSeqN traceValSeq
      traceValSeqFn traceValSeqN traceValSeqNFn traceShowVal
--- a/lib/licenses.nix
+++ b/lib/licenses.nix
@ -355,6 +355,11 @@ lib.mapAttrs (n: v: v // { shortName = n; }) rec {
    fullName = "Independent JPEG Group License";
  };

+  imagemagick = spdx {
+    fullName = "ImageMagick License";
+    spdxId = "imagemagick";
+  };
+
  inria-compcert = {
    fullName  = "INRIA Non-Commercial License Agreement for the CompCert verified compiler";
    url       = "http://compcert.inria.fr/doc/LICENSE";
--- a/lib/lists.nix
+++ b/lib/lists.nix
@ -509,7 +509,8 @@ rec {
       => 3
  */
  last = list:
-    assert list != []; elemAt list (length list - 1);
+    assert lib.assertMsg (list != []) "lists.last: list must not be empty!";
+    elemAt list (length list - 1);

  /* Return all elements but the last

@ -517,7 +518,9 @@ rec {
       init [ 1 2 3 ]
       => [ 1 2 ]
  */
-  init = list: assert list != []; take (length list - 1) list;
+  init = list:
+    assert lib.assertMsg (list != []) "lists.init: list must not be empty!";
+    take (length list - 1) list;


  /* return the image of the cross product of some lists by a function
--- a/lib/strings.nix
+++ b/lib/strings.nix
@ -410,7 +410,7 @@ rec {
      components = splitString "/" url;
      filename = lib.last components;
      name = builtins.head (splitString sep filename);
-    in assert name !=  filename; name;
+    in assert name != filename; name;

  /* Create an --{enable,disable}-<feat> string that can be passed to
     standard GNU Autoconf scripts.
@ -468,7 +468,10 @@ rec {
      strw = lib.stringLength str;
      reqWidth = width - (lib.stringLength filler);
    in
-      assert strw <= width;
+      assert lib.assertMsg (strw <= width)
+        "fixedWidthString: requested string length (${
+          toString width}) must not be shorter than actual length (${
+            toString strw})";
      if strw == width then str else filler + fixedWidthString reqWidth filler str;

  /* Format a number adding leading zeroes up to fixed width.
@ -501,7 +504,7 @@ rec {
  isStorePath = x:
       isCoercibleToString x
    && builtins.substring 0 1 (toString x) == "/"
-    && dirOf (builtins.toPath x) == builtins.storeDir;
+    && dirOf x == builtins.storeDir;

  /* Convert string to int
     Obviously, it is a bit hacky to use fromJSON that way.
@ -537,11 +540,10 @@ rec {
  */
  readPathsFromFile = rootPath: file:
    let
-      root = toString rootPath;
      lines = lib.splitString "\n" (builtins.readFile file);
      removeComments = lib.filter (line: line != "" && !(lib.hasPrefix "#" line));
      relativePaths = removeComments lines;
-      absolutePaths = builtins.map (path: builtins.toPath (root + "/" + path)) relativePaths;
+      absolutePaths = builtins.map (path: rootPath + "/${path}") relativePaths;
    in
      absolutePaths;

--- a/lib/tests/misc.nix
+++ b/lib/tests/misc.nix
@ -112,7 +112,7 @@ runTests {
        storePathAppendix = isStorePath
          "${goodPath}/bin/python";
        nonAbsolute = isStorePath (concatStrings (tail (stringToCharacters goodPath)));
-        asPath = isStorePath (builtins.toPath goodPath);
+        asPath = isStorePath goodPath;
        otherPath = isStorePath "/something/else";
        otherVals = {
          attrset = isStorePath {};
@ -357,7 +357,7 @@ runTests {
      int = 42;
      bool = true;
      string = ''fno"rd'';
-      path = /. + "/foo"; # toPath returns a string
+      path = /. + "/foo";
      null_ = null;
      function = x: x;
      functionArgs = { arg ? 4, foo }: arg;
--- a/lib/trivial.nix
+++ b/lib/trivial.nix
@ -171,7 +171,7 @@ rec {
    builtins.fromJSON (builtins.readFile path);


-  ## Warnings and asserts
+  ## Warnings

  /* See https://github.com/NixOS/nix/issues/749. Eventually we'd like these
     to expand to Nix builtins that carry metadata so that Nix can filter out
--- a/lib/types.nix
+++ b/lib/types.nix
@ -119,7 +119,9 @@ rec {
      let
        betweenDesc = lowest: highest:
          "${toString lowest} and ${toString highest} (both inclusive)";
-        between = lowest: highest: assert lowest <= highest;
+        between = lowest: highest:
+          assert lib.assertMsg (lowest <= highest)
+            "ints.between: lowest must be smaller than highest";
          addCheck int (x: x >= lowest && x <= highest) // {
            name = "intBetween";
            description = "integer between ${betweenDesc lowest highest}";
@ -439,7 +441,9 @@ rec {
    # Either value of type `finalType` or `coercedType`, the latter is
    # converted to `finalType` using `coerceFunc`.
    coercedTo = coercedType: coerceFunc: finalType:
-      assert coercedType.getSubModules == null;
+      assert lib.assertMsg (coercedType.getSubModules == null)
+        "coercedTo: coercedType must not have submodules (it’s a ${
+          coercedType.description})";
      mkOptionType rec {
        name = "coercedTo";
        description = "${finalType.description} or ${coercedType.description} convertible to it";
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@ -3893,6 +3893,11 @@
    github = "StillerHarpo";
    name = "Florian Engel";
  };
+  stites = {
+    email = "sam@stites.io";
+    github = "stites";
+    name = "Sam Stites";
+  };
  stumoss = {
    email = "samoss@gmail.com";
    github = "stumoss";
@ -4158,6 +4163,11 @@
    github = "tomsmeets";
    name = "Tom Smeets";
  };
+  toonn = {
+    email = "nnoot@toonn.io";
+    github = "toonn";
+    name = "Toon Nolten";
+  };
  travisbhartwell = {
    email = "nafai@travishartwell.net";
    github = "travisbhartwell";
--- a/nixos/doc/manual/release-notes/rl-1809.xml
+++ b/nixos/doc/manual/release-notes/rl-1809.xml
@ -283,6 +283,14 @@ $ nix-instantiate -E '(import &lt;nixpkgsunstable&gt; {}).gitFull'
      from your config without any issues.
    </para>
   </listitem>
+   <listitem>
+    <para>
+      <literal>stdenv.system</literal> and <literal>system</literal> in nixpkgs now refer to the host platform instead of the build platform.
+      For native builds this is not change, let alone a breaking one.
+      For cross builds, it is a breaking change, and <literal>stdenv.buildPlatform.system</literal> can be used instead for the old behavior.
+      They should be using that anyways for clarity.
+    </para>
+   </listitem>
  </itemizedlist>
 </section>

@ -536,6 +544,13 @@ inherit (pkgs.nixos {
      a new paragraph.
    </para>
  </listitem>
+  <listitem>
+    <para>
+      Top-level <literal>buildPlatform</literal>, <literal>hostPlatform</literal>, and <literal>targetPlatform</literal> in Nixpkgs are deprecated.
+      Please use their equivalents in <literal>stdenv</literal> instead:
+      <literal>stdenv.buildPlatform</literal>, <literal>stdenv.hostPlatform</literal>, and <literal>stdenv.targetPlatform</literal>.
+    </para>
+  </listitem>
  </itemizedlist>
 </section>
 </section>
--- a/nixos/lib/eval-config.nix
+++ b/nixos/lib/eval-config.nix
@ -28,7 +28,7 @@

 let extraArgs_ = extraArgs; pkgs_ = pkgs;
    extraModules = let e = builtins.getEnv "NIXOS_EXTRA_MODULE_PATH";
-                   in if e == "" then [] else [(import (builtins.toPath e))];
+                   in if e == "" then [] else [(import e)];
 in

 let
@ -36,7 +36,11 @@ let
    _file = ./eval-config.nix;
    key = _file;
    config = {
-      nixpkgs.localSystem = lib.mkDefault { inherit system; };
+      # Explicit `nixpkgs.system` or `nixpkgs.localSystem` should override
+      # this.  Since the latter defaults to the former, the former should
+      # default to the argument. That way this new default could propagate all
+      # they way through, but has the last priority behind everything else.
+      nixpkgs.system = lib.mkDefault system;
      _module.args.pkgs = lib.mkIf (pkgs_ != null) (lib.mkForce pkgs_);
    };
  };
--- a/nixos/modules/config/shells-environment.nix
+++ b/nixos/modules/config/shells-environment.nix
@ -163,15 +163,24 @@ in
        /bin/sh
      '';

+    # For resetting environment with `. /etc/set-environment` when needed
+    # and discoverability (see motivation of #30418).
+    environment.etc."set-environment".source = config.system.build.setEnvironment;
+
    system.build.setEnvironment = pkgs.writeText "set-environment"
-       ''
-         ${exportedEnvVars}
+      ''
+        # DO NOT EDIT -- this file has been generated automatically.

-         ${cfg.extraInit}
+        # Prevent this file from being sourced by child shells.
+        export __NIXOS_SET_ENVIRONMENT_DONE=1

-         # ~/bin if it exists overrides other bin directories.
-         export PATH="$HOME/bin:$PATH"
-       '';
+        ${exportedEnvVars}
+
+        ${cfg.extraInit}
+
+        # ~/bin if it exists overrides other bin directories.
+        export PATH="$HOME/bin:$PATH"
+      '';

    system.activationScripts.binsh = stringAfter [ "stdio" ]
      ''
--- a/nixos/modules/config/xdg/mime.nix
+++ b/nixos/modules/config/xdg/mime.nix
@ -7,7 +7,7 @@ with lib;
      type = types.bool;
      default = true;
      description = ''
-        Whether to install files to support the 
+        Whether to install files to support the
        <link xlink:href="https://specifications.freedesktop.org/shared-mime-info-spec/shared-mime-info-spec-latest.html">XDG Shared MIME-info specification</link> and the
        <link xlink:href="https://specifications.freedesktop.org/mime-apps-spec/mime-apps-spec-latest.html">XDG MIME Applications specification</link>.
      '';
@ -17,18 +17,18 @@ with lib;
  config = mkIf config.xdg.mime.enable {
    environment.pathsToLink = [ "/share/mime" ];

-    environment.systemPackages = [ 
-      # this package also installs some useful data, as well as its utilities 
-      pkgs.shared-mime-info 
+    environment.systemPackages = [
+      # this package also installs some useful data, as well as its utilities
+      pkgs.shared-mime-info
    ];

    environment.extraSetup = ''
-      if [ -w $out/share/mime ]; then
-        XDG_DATA_DIRS=$out/share ${pkgs.shared-mime-info}/bin/update-mime-database -V $out/share/mime > /dev/null
+      if [ -w $out/share/mime ] && [ -d $out/share/mime/packages ]; then
+          XDG_DATA_DIRS=$out/share ${pkgs.shared-mime-info}/bin/update-mime-database -V $out/share/mime > /dev/null
      fi

      if [ -w $out/share/applications ]; then
-        ${pkgs.desktop-file-utils}/bin/update-desktop-database $out/share/applications
+          ${pkgs.desktop-file-utils}/bin/update-desktop-database $out/share/applications
      fi
    '';
  };
--- a/nixos/modules/misc/nixpkgs.nix
+++ b/nixos/modules/misc/nixpkgs.nix
@ -62,12 +62,11 @@ in
    pkgs = mkOption {
      defaultText = literalExample
        ''import "''${nixos}/.." {
-            inherit (config.nixpkgs) config overlays localSystem crossSystem;
+            inherit (cfg) config overlays localSystem crossSystem;
          }
        '';
      default = import ../../.. {
-        localSystem = { inherit (cfg) system; } // cfg.localSystem;
-        inherit (cfg) config overlays crossSystem;
+        inherit (cfg) config overlays localSystem crossSystem;
      };
      type = pkgsType;
      example = literalExample ''import <nixpkgs> {}'';
@ -140,8 +139,11 @@ in

    localSystem = mkOption {
      type = types.attrs; # TODO utilize lib.systems.parsedPlatform
-      default = { system = builtins.currentSystem; };
+      default = { inherit (cfg) system; };
      example = { system = "aarch64-linux"; config = "aarch64-unknown-linux-gnu"; };
+      # Make sure that the final value has all fields for sake of other modules
+      # referring to this. TODO make `lib.systems` itself use the module system.
+      apply = lib.systems.elaborate;
      defaultText = literalExample
        ''(import "''${nixos}/../lib").lib.systems.examples.aarch64-multiplatform'';
      description = ''
@ -180,6 +182,7 @@ in
    system = mkOption {
      type = types.str;
      example = "i686-linux";
+      default = { system = builtins.currentSystem; };
      description = ''
        Specifies the Nix platform type on which NixOS should be built.
        It is better to specify <code>nixpkgs.localSystem</code> instead.
@ -196,6 +199,7 @@ in
        </programlisting>
        See <code>nixpkgs.localSystem</code> for more information.

+        Ignored when <code>nixpkgs.localSystem</code> is set.
        Ignored when <code>nixpkgs.pkgs</code> is set.
      '';
    };
--- a/nixos/modules/module-list.nix
+++ b/nixos/modules/module-list.nix
@ -245,6 +245,7 @@
  ./services/desktops/gnome3/gnome-user-share.nix
  ./services/desktops/gnome3/gpaste.nix
  ./services/desktops/gnome3/gvfs.nix
+  ./services/desktops/gnome3/rygel.nix
  ./services/desktops/gnome3/seahorse.nix
  ./services/desktops/gnome3/sushi.nix
  ./services/desktops/gnome3/tracker.nix
@ -406,6 +407,7 @@
  ./services/misc/taskserver
  ./services/misc/tzupdate.nix
  ./services/misc/uhub.nix
+  ./services/misc/weechat.nix
  ./services/misc/xmr-stak.nix
  ./services/misc/zookeeper.nix
  ./services/monitoring/apcupsd.nix
@ -518,6 +520,7 @@
  ./services/networking/i2pd.nix
  ./services/networking/i2p.nix
  ./services/networking/iodine.nix
+  ./services/networking/iperf3.nix
  ./services/networking/ircd-hybrid/default.nix
  ./services/networking/iwd.nix
  ./services/networking/keepalived/default.nix
--- a/nixos/modules/programs/bash/bash.nix
+++ b/nixos/modules/programs/bash/bash.nix
@ -126,7 +126,9 @@ in
    programs.bash = {

      shellInit = ''
-        ${config.system.build.setEnvironment.text}
+        if [ -z "$__NIXOS_SET_ENVIRONMENT_DONE" ]; then
+            . ${config.system.build.setEnvironment}
+        fi

        ${cfge.shellInit}
      '';
@ -166,11 +168,11 @@ in

        # Read system-wide modifications.
        if test -f /etc/profile.local; then
-          . /etc/profile.local
+            . /etc/profile.local
        fi

        if [ -n "''${BASH_VERSION:-}" ]; then
-          . /etc/bashrc
+            . /etc/bashrc
        fi
      '';

@ -191,12 +193,12 @@ in

        # We are not always an interactive shell.
        if [ -n "$PS1" ]; then
-          ${cfg.interactiveShellInit}
+            ${cfg.interactiveShellInit}
        fi

        # Read system-wide modifications.
        if test -f /etc/bashrc.local; then
-          . /etc/bashrc.local
+            . /etc/bashrc.local
        fi
      '';

--- a/nixos/modules/programs/fish.nix
+++ b/nixos/modules/programs/fish.nix
@ -27,7 +27,7 @@ in
        '';
        type = types.bool;
      };
-      
+
      vendor.config.enable = mkOption {
        type = types.bool;
        default = true;
@ -43,7 +43,7 @@ in
          Whether fish should use completion files provided by other packages.
        '';
      };
-      
+
      vendor.functions.enable = mkOption {
        type = types.bool;
        default = true;
@ -107,9 +107,11 @@ in
      # This happens before $__fish_datadir/config.fish sets fish_function_path, so it is currently
      # unset. We set it and then completely erase it, leaving its configuration to $__fish_datadir/config.fish
      set fish_function_path ${pkgs.fish-foreign-env}/share/fish-foreign-env/functions $__fish_datadir/functions
-      
+
      # source the NixOS environment config
-      fenv source ${config.system.build.setEnvironment}
+      if [ -z "$__NIXOS_SET_ENVIRONMENT_DONE" ]
+          fenv source ${config.system.build.setEnvironment}
+      end

      # clear fish_function_path so that it will be correctly set when we return to $__fish_datadir/config.fish
      set -e fish_function_path
@ -123,7 +125,7 @@ in
        set fish_function_path ${pkgs.fish-foreign-env}/share/fish-foreign-env/functions $fish_function_path
        fenv source /etc/fish/foreign-env/shellInit > /dev/null
        set -e fish_function_path[1]
-        
+
        ${cfg.shellInit}

        # and leave a note so we don't source this config section again from
@ -137,7 +139,7 @@ in
        set fish_function_path ${pkgs.fish-foreign-env}/share/fish-foreign-env/functions $fish_function_path
        fenv source /etc/fish/foreign-env/loginShellInit > /dev/null
        set -e fish_function_path[1]
-        
+
        ${cfg.loginShellInit}

        # and leave a note so we don't source this config section again from
@ -149,12 +151,11 @@ in
      status --is-interactive; and not set -q __fish_nixos_interactive_config_sourced
      and begin
        ${fishAliases}
-        

        set fish_function_path ${pkgs.fish-foreign-env}/share/fish-foreign-env/functions $fish_function_path
        fenv source /etc/fish/foreign-env/interactiveShellInit > /dev/null
        set -e fish_function_path[1]
-        
+
        ${cfg.promptInit}
        ${cfg.interactiveShellInit}

@ -170,7 +171,7 @@ in
      ++ optional cfg.vendor.config.enable "/share/fish/vendor_conf.d"
      ++ optional cfg.vendor.completions.enable "/share/fish/vendor_completions.d"
      ++ optional cfg.vendor.functions.enable "/share/fish/vendor_functions.d";
-    
+
    environment.systemPackages = [ pkgs.fish ];

    environment.shells = [
--- a/nixos/modules/programs/zsh/zsh.nix
+++ b/nixos/modules/programs/zsh/zsh.nix
@ -70,7 +70,7 @@ in
      promptInit = mkOption {
        default = ''
          if [ "$TERM" != dumb ]; then
-            autoload -U promptinit && promptinit && prompt walters
+              autoload -U promptinit && promptinit && prompt walters
          fi
        '';
        description = ''
@ -116,7 +116,9 @@ in
        if [ -n "$__ETC_ZSHENV_SOURCED" ]; then return; fi
        export __ETC_ZSHENV_SOURCED=1

-        ${config.system.build.setEnvironment.text}
+        if [ -z "$__NIXOS_SET_ENVIRONMENT_DONE" ]; then
+            . ${config.system.build.setEnvironment}
+        fi

        ${cfge.shellInit}

@ -124,7 +126,7 @@ in

        # Read system-wide modifications.
        if test -f /etc/zshenv.local; then
-          . /etc/zshenv.local
+            . /etc/zshenv.local
        fi
      '';

@ -143,7 +145,7 @@ in

        # Read system-wide modifications.
        if test -f /etc/zprofile.local; then
-          . /etc/zprofile.local
+            . /etc/zprofile.local
        fi
      '';

@ -169,7 +171,7 @@ in

        # Tell zsh how to find installed completions
        for p in ''${(z)NIX_PROFILES}; do
-          fpath+=($p/share/zsh/site-functions $p/share/zsh/$ZSH_VERSION/functions $p/share/zsh/vendor-completions)
+            fpath+=($p/share/zsh/site-functions $p/share/zsh/$ZSH_VERSION/functions $p/share/zsh/vendor-completions)
        done

        ${optionalString cfg.enableGlobalCompInit "autoload -U compinit && compinit"}
@ -184,7 +186,7 @@ in

        # Read system-wide modifications.
        if test -f /etc/zshrc.local; then
-          . /etc/zshrc.local
+            . /etc/zshrc.local
        fi
      '';

--- a/nixos/modules/services/computing/slurm/slurm.nix
+++ b/nixos/modules/services/computing/slurm/slurm.nix
@ -8,6 +8,7 @@ let
  # configuration file can be generated by http://slurm.schedmd.com/configurator.html
  configFile = pkgs.writeTextDir "slurm.conf"
    ''
+      ClusterName=${cfg.clusterName}
      ${optionalString (cfg.controlMachine != null) ''controlMachine=${cfg.controlMachine}''}
      ${optionalString (cfg.controlAddr != null) ''controlAddr=${cfg.controlAddr}''}
      ${optionalString (cfg.nodeName != null) ''nodeName=${cfg.nodeName}''}
@ -105,6 +106,15 @@ in
        '';
      };

+      clusterName = mkOption {
+        type = types.str;
+        default = "default";
+        example = "myCluster";
+        description = ''
+          Necessary to distinguish accounting records in a multi-cluster environment.
+        '';
+      };
+
      nodeName = mkOption {
        type = types.nullOr types.str;
        default = null;
--- a/nixos/modules/services/desktops/gnome3/rygel.nix
+++ b/nixos/modules/services/desktops/gnome3/rygel.nix
@ -0,0 +1,30 @@
+# rygel service.
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+{
+  ###### interface
+  options = {
+    services.gnome3.rygel = {
+      enable = mkOption {
+        default = false;
+        description = ''
+          Whether to enable Rygel UPnP Mediaserver.
+
+          You will need to also allow UPnP connections in firewall, see the following <link xlink:href="https://github.com/NixOS/nixpkgs/pull/45045#issuecomment-416030795">comment</link>.
+        '';
+        type = types.bool;
+      };
+    };
+  };
+
+  ###### implementation
+  config = mkIf config.services.gnome3.rygel.enable {
+    environment.systemPackages = [ pkgs.gnome3.rygel ];
+
+    services.dbus.packages = [ pkgs.gnome3.rygel ];
+
+    systemd.packages = [ pkgs.gnome3.rygel ];
+  };
+}
--- a/nixos/modules/services/misc/weechat.nix
+++ b/nixos/modules/services/misc/weechat.nix
@ -0,0 +1,56 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+  cfg = config.services.weechat;
+in
+
+{
+  options.services.weechat = {
+    enable = mkEnableOption "weechat";
+    root = mkOption {
+      description = "Weechat state directory.";
+      type = types.str;
+      default = "/var/lib/weechat";
+    };
+    sessionName = mkOption {
+      description = "Name of the `screen' session for weechat.";
+      default = "weechat-screen";
+      type = types.str;
+    };
+    binary = mkOption {
+      description = "Binary to execute (by default \${weechat}/bin/weechat).";
+      example = literalExample ''
+        ''${pkgs.weechat}/bin/weechat-headless
+      '';
+      default = "${pkgs.weechat}/bin/weechat";
+    };
+  };
+
+  config = mkIf cfg.enable {
+    users = {
+      groups.weechat = {};
+      users.weechat = {
+        createHome = true;
+        group = "weechat";
+        home = cfg.root;
+        isSystemUser = true;
+      };
+    };
+
+    systemd.services.weechat = {
+      environment.WEECHAT_HOME = cfg.root;
+      serviceConfig = {
+        User = "weechat";
+        Group = "weechat";
+        RemainAfterExit = "yes";
+      };
+      script = "exec ${pkgs.screen}/bin/screen -Dm -S ${cfg.sessionName} ${cfg.binary}";
+      wantedBy = [ "multi-user.target" ];
+      wants = [ "network.target" ];
+    };
+  };
+
+  meta.doc = ./weechat.xml;
+}
--- a/nixos/modules/services/misc/weechat.xml
+++ b/nixos/modules/services/misc/weechat.xml
@ -0,0 +1,61 @@
+<chapter xmlns="http://docbook.org/ns/docbook"
+         xmlns:xlink="http://www.w3.org/1999/xlink"
+         xmlns:xi="http://www.w3.org/2001/XInclude"
+         version="5.0"
+         xml:id="module-services-weechat">
+
+<title>WeeChat</title>
+<para><link xlink:href="https://weechat.org/">WeeChat</link> is a fast and extensible IRC client.</para>
+
+<section><title>Basic Usage</title>
+<para>
+By default, the module creates a
+<literal><link xlink:href="https://www.freedesktop.org/wiki/Software/systemd/">systemd</link></literal> unit
+which runs the chat client in a detached
+<literal><link xlink:href="https://www.gnu.org/software/screen/">screen</link></literal> session.
+
+</para>
+
+<para>
+This can be done by enabling the <literal>weechat</literal> service:
+
+<programlisting>
+{ ... }:
+
+{
+  <link linkend="opt-services.weechat.enable">services.weechat.enable</link> = true;
+}
+</programlisting>
+</para>
+<para>
+The service is managed by a dedicated user
+named <literal>weechat</literal> in the state directory
+<literal>/var/lib/weechat</literal>.
+</para>
+</section>
+<section><title>Re-attaching to WeeChat</title>
+<para>
+WeeChat runs in a screen session owned by a dedicated user. To explicitly
+allow your another user to attach to this session, the <literal>screenrc</literal> needs to be tweaked
+by adding <link xlink:href="https://www.gnu.org/software/screen/manual/html_node/Multiuser.html#Multiuser">multiuser</link> support:
+
+<programlisting>
+{
+  <link linkend="opt-programs.screen.screenrc">programs.screen.screenrc</link> = ''
+    multiuser on
+    acladd normal_user
+  '';
+}
+</programlisting>
+
+Now, the session can be re-attached like this:
+
+<programlisting>
+screen -r weechat-screen
+</programlisting>
+</para>
+<para>
+<emphasis>The session name can be changed using <link linkend="opt-services.weechat.sessionName">services.weechat.sessionName.</link></emphasis>
+</para>
+</section>
+</chapter>
--- a/nixos/modules/services/monitoring/riemann.nix
+++ b/nixos/modules/services/monitoring/riemann.nix
@ -17,9 +17,9 @@ let

  launcher = writeScriptBin "riemann" ''
    #!/bin/sh
-    exec ${jdk}/bin/java ${concatStringsSep "\n" cfg.extraJavaOpts} \
+    exec ${jdk}/bin/java ${concatStringsSep " " cfg.extraJavaOpts} \
      -cp ${classpath} \
-      riemann.bin ${writeText "riemann-config.clj" riemannConfig}
+      riemann.bin ${cfg.configFile}
  '';

 in {
@ -37,7 +37,8 @@ in {
      config = mkOption {
        type = types.lines;
        description = ''
-          Contents of the Riemann configuration file.
+          Contents of the Riemann configuration file. For more complicated
+          config you should use configFile.
        '';
      };
      configFiles = mkOption {
@ -47,7 +48,15 @@ in {
          Extra files containing Riemann configuration. These files will be
          loaded at runtime by Riemann (with Clojure's
          <literal>load-file</literal> function) at the end of the
-          configuration.
+          configuration if you use the config option, this is ignored if you
+          use configFile.
+        '';
+      };
+      configFile = mkOption {
+        type = types.str;
+        description = ''
+          A Riemann config file. Any files in the same directory as this file
+          will be added to the classpath by Riemann.
        '';
      };
      extraClasspathEntries = mkOption {
@ -77,6 +86,10 @@ in {
      group = "riemann";
    };

+    services.riemann.configFile = mkDefault (
+      writeText "riemann-config.clj" riemannConfig
+    );
+
    systemd.services.riemann = {
      wantedBy = [ "multi-user.target" ];
      path = [ inetutils ];
@ -84,6 +97,7 @@ in {
        User = "riemann";
        ExecStart = "${launcher}/bin/riemann";
      };
+      serviceConfig.LimitNOFILE = 65536;
    };

  };
--- a/nixos/modules/services/networking/i2pd.nix
+++ b/nixos/modules/services/networking/i2pd.nix
@ -8,6 +8,17 @@ let

  homeDir = "/var/lib/i2pd";

+  strOpt = k: v: k + " = " + v;
+  boolOpt = k: v: k + " = " + boolToString v;
+  intOpt = k: v: k + " = " + toString v;
+  lstOpt = k: xs: k + " = " + concatStringsSep "," xs;
+  optionalNullString = o: s: optional (! isNull s) (strOpt o s);
+  optionalNullBool = o: b: optional (! isNull b) (boolOpt o b);
+  optionalNullInt = o: i: optional (! isNull i) (intOpt o i);
+  optionalEmptyList = o: l: optional ([] != l) (lstOpt o l);
+
+  mkEnableTrueOption = name: mkEnableOption name // { default = true; };
+
  mkEndpointOpt = name: addr: port: {
    enable = mkEnableOption name;
    name = mkOption {
@ -18,42 +29,54 @@ let
    address = mkOption {
      type = types.str;
      default = addr;
-      description = "Bind address for ${name} endpoint. Default: " + addr;
+      description = "Bind address for ${name} endpoint.";
    };
    port = mkOption {
      type = types.int;
      default = port;
-      description = "Bind port for ${name} endoint. Default: " + toString port;
+      description = "Bind port for ${name} endoint.";
    };
  };

-  mkKeyedEndpointOpt = name: addr: port: keyFile:
+  i2cpOpts = name: {
+    length = mkOption {
+      type = types.int;
+      description = "Guaranteed minimum hops for ${name} tunnels.";
+      default = 3;
+    };
+    quantity = mkOption {
+      type = types.int;
+      description = "Number of simultaneous ${name} tunnels.";
+      default = 5;
+    };
+  };
+
+  mkKeyedEndpointOpt = name: addr: port: keyloc:
    (mkEndpointOpt name addr port) // {
      keys = mkOption {
-        type = types.str;
-        default = "";
+        type = with types; nullOr str;
+        default = keyloc;
        description = ''
          File to persist ${lib.toUpper name} keys.
        '';
      };
+      inbound = i2cpOpts name;
+      outbound = i2cpOpts name;
+      latency.min = mkOption {
+        type = with types; nullOr int;
+        description = "Min latency for tunnels.";
+        default = null;
+      };
+      latency.max = mkOption {
+        type = with types; nullOr int;
+        description = "Max latency for tunnels.";
+        default = null;
+      };
    };

-  commonTunOpts = let
-    i2cpOpts = {
-      length = mkOption {
-        type = types.int;
-        description = "Guaranteed minimum hops.";
-        default = 3;
-      };
-      quantity = mkOption {
-        type = types.int;
-        description = "Number of simultaneous tunnels.";
-        default = 5;
-      };
-    };
-  in name: {
-    outbound = i2cpOpts;
-    inbound = i2cpOpts;
+  commonTunOpts = name: {
+    outbound = i2cpOpts name;
+    inbound = i2cpOpts name;
    crypto.tagsToSend = mkOption {
      type = types.int;
      description = "Number of ElGamal/AES tags to send.";
@ -70,94 +93,142 @@ let
    };
  } // mkEndpointOpt name "127.0.0.1" 0;

-  i2pdConf = pkgs.writeText "i2pd.conf" ''
-    # DO NOT EDIT -- this file has been generated automatically.
-    loglevel = ${cfg.logLevel}
-
-    ipv4 = ${boolToString cfg.enableIPv4}
-    ipv6 = ${boolToString cfg.enableIPv6}
-    notransit = ${boolToString cfg.notransit}
-    floodfill = ${boolToString cfg.floodfill}
-    netid = ${toString cfg.netid}
-    ${if isNull cfg.bandwidth then "" else "bandwidth = ${toString cfg.bandwidth}" }
-    ${if isNull cfg.port then "" else "port = ${toString cfg.port}"}
-
-    [limits]
-    transittunnels = ${toString cfg.limits.transittunnels}
-
-    [upnp]
-    enabled = ${boolToString cfg.upnp.enable}
-    name = ${cfg.upnp.name}
-
-    [precomputation]
-    elgamal = ${boolToString cfg.precomputation.elgamal}
-
-    [reseed]
-    verify = ${boolToString cfg.reseed.verify}
-    file = ${cfg.reseed.file}
-    urls = ${builtins.concatStringsSep "," cfg.reseed.urls}
-
-    [addressbook]
-    defaulturl = ${cfg.addressbook.defaulturl}
-    subscriptions = ${builtins.concatStringsSep "," cfg.addressbook.subscriptions}
-
-    ${flip concatMapStrings
+  sec = name: "\n[" + name + "]";
+  notice = "# DO NOT EDIT -- this file has been generated automatically.";
+  i2pdConf = let
+    opts = [
+      notice
+      (strOpt "loglevel" cfg.logLevel)
+      (boolOpt "logclftime" cfg.logCLFTime)
+      (boolOpt "ipv4" cfg.enableIPv4)
+      (boolOpt "ipv6" cfg.enableIPv6)
+      (boolOpt "notransit" cfg.notransit)
+      (boolOpt "floodfill" cfg.floodfill)
+      (intOpt "netid" cfg.netid)
+    ] ++ (optionalNullInt "bandwidth" cfg.bandwidth)
+      ++ (optionalNullInt "port" cfg.port)
+      ++ (optionalNullString "family" cfg.family)
+      ++ (optionalNullString "datadir" cfg.dataDir)
+      ++ (optionalNullInt "share" cfg.share)
+      ++ (optionalNullBool "ssu" cfg.ssu)
+      ++ (optionalNullBool "ntcp" cfg.ntcp)
+      ++ (optionalNullString "ntcpproxy" cfg.ntcpProxy)
+      ++ (optionalNullString "ifname" cfg.ifname)
+      ++ (optionalNullString "ifname4" cfg.ifname4)
+      ++ (optionalNullString "ifname6" cfg.ifname6)
+      ++ [
+      (sec "limits")
+      (intOpt "transittunnels" cfg.limits.transittunnels)
+      (intOpt "coresize" cfg.limits.coreSize)
+      (intOpt "openfiles" cfg.limits.openFiles)
+      (intOpt "ntcphard" cfg.limits.ntcpHard)
+      (intOpt "ntcpsoft" cfg.limits.ntcpSoft)
+      (intOpt "ntcpthreads" cfg.limits.ntcpThreads)
+      (sec "upnp")
+      (boolOpt "enabled" cfg.upnp.enable)
+      (sec "precomputation")
+      (boolOpt "elgamal" cfg.precomputation.elgamal)
+      (sec "reseed")
+      (boolOpt "verify" cfg.reseed.verify)
+    ] ++ (optionalNullString "file" cfg.reseed.file)
+      ++ (optionalEmptyList "urls" cfg.reseed.urls)
+      ++ (optionalNullString "floodfill" cfg.reseed.floodfill)
+      ++ (optionalNullString "zipfile" cfg.reseed.zipfile)
+      ++ (optionalNullString "proxy" cfg.reseed.proxy)
+      ++ [
+      (sec "trust")
+      (boolOpt "enabled" cfg.trust.enable)
+      (boolOpt "hidden" cfg.trust.hidden)
+    ] ++ (optionalEmptyList "routers" cfg.trust.routers)
+      ++ (optionalNullString "family" cfg.trust.family)
+      ++ [
+      (sec "websockets")
+      (boolOpt "enabled" cfg.websocket.enable)
+      (strOpt "address" cfg.websocket.address)
+      (intOpt "port" cfg.websocket.port)
+      (sec "exploratory")
+      (intOpt "inbound.length" cfg.exploratory.inbound.length)
+      (intOpt "inbound.quantity" cfg.exploratory.inbound.quantity)
+      (intOpt "outbound.length" cfg.exploratory.outbound.length)
+      (intOpt "outbound.quantity" cfg.exploratory.outbound.quantity)
+      (sec "ntcp2")
+      (boolOpt "enabled" cfg.ntcp2.enable)
+      (boolOpt "published" cfg.ntcp2.published)
+      (intOpt "port" cfg.ntcp2.port)
+      (sec "addressbook")
+      (strOpt "defaulturl" cfg.addressbook.defaulturl)
+    ] ++ (optionalEmptyList "subscriptions" cfg.addressbook.subscriptions)
+      ++ (flip map
      (collect (proto: proto ? port && proto ? address && proto ? name) cfg.proto)
-      (proto: ''
-        [${proto.name}]
-        enabled = ${boolToString proto.enable}
-        address = ${proto.address}
-        port = ${toString proto.port}
-        ${if proto ? keys then "keys = ${proto.keys}" else ""}
-        ${if proto ? auth then "auth = ${boolToString proto.auth}" else ""}
-        ${if proto ? user then "user = ${proto.user}" else ""}
-        ${if proto ? pass then "pass = ${proto.pass}" else ""}
-        ${if proto ? outproxy then "outproxy = ${proto.outproxy}" else ""}
-        ${if proto ? outproxyPort then "outproxyport = ${toString proto.outproxyPort}" else ""}
-      '')
-    }
-  '';
+      (proto: let protoOpts = [
+        (sec proto.name)
+        (boolOpt "enabled" proto.enable)
+        (strOpt "address" proto.address)
+        (intOpt "port" proto.port)
+        ] ++ (if proto ? keys then optionalNullString "keys" proto.keys else [])
+        ++ (if proto ? auth then optionalNullBool "auth" proto.auth else [])
+        ++ (if proto ? user then optionalNullString "user" proto.user else [])
+        ++ (if proto ? pass then optionalNullString "pass" proto.pass else [])
+        ++ (if proto ? strictHeaders then optionalNullBool "strictheaders" proto.strictHeaders else [])
+        ++ (if proto ? hostname then optionalNullString "hostname" proto.hostname else [])
+        ++ (if proto ? outproxy then optionalNullString "outproxy" proto.outproxy else [])
+        ++ (if proto ? outproxyPort then optionalNullInt "outproxyport" proto.outproxyPort else [])
+        ++ (if proto ? outproxyEnable then optionalNullBool "outproxy.enabled" proto.outproxyEnable else []);
+        in (concatStringsSep "\n" protoOpts)
+      ));
+  in
+    pkgs.writeText "i2pd.conf" (concatStringsSep "\n" opts);

-  i2pdTunnelConf = pkgs.writeText "i2pd-tunnels.conf" ''
-    # DO NOT EDIT -- this file has been generated automatically.
-    ${flip concatMapStrings
+  tunnelConf = let opts = [
+    notice
+    (flip map
      (collect (tun: tun ? port && tun ? destination) cfg.outTunnels)
-      (tun: ''
-        [${tun.name}]
-        type = client
-        destination = ${tun.destination}
-        destinationport = ${toString tun.destinationPort}
-        keys = ${tun.keys}
-        address = ${tun.address}
-        port = ${toString tun.port}
-        inbound.length = ${toString tun.inbound.length}
-        outbound.length = ${toString tun.outbound.length}
-        inbound.quantity = ${toString tun.inbound.quantity}
-        outbound.quantity = ${toString tun.outbound.quantity}
-        crypto.tagsToSend = ${toString tun.crypto.tagsToSend}
-      '')
-    }
-    ${flip concatMapStrings
+      (tun: let outTunOpts = [
+        (sec tun.name)
+        "type = client"
+        (intOpt "port" tun.port)
+        (strOpt "destination" tun.destination)
+        ] ++ (if tun ? destinationPort then optionalNullInt "destinationport" tun.destinationPort else [])
+        ++ (if tun ? keys then
+            optionalNullString "keys" tun.keys else [])
+        ++ (if tun ? address then
+            optionalNullString "address" tun.address else [])
+        ++ (if tun ? inbound.length then
+            optionalNullInt "inbound.length" tun.inbound.length else [])
+        ++ (if tun ? inbound.quantity then
+            optionalNullInt "inbound.quantity" tun.inbound.quantity else [])
+        ++ (if tun ? outbound.length then
+            optionalNullInt "outbound.length" tun.outbound.length else [])
+        ++ (if tun ? outbound.quantity then
+            optionalNullInt "outbound.quantity" tun.outbound.quantity else [])
+        ++ (if tun ? crypto.tagsToSend then
+            optionalNullInt "crypto.tagstosend" tun.crypto.tagsToSend else []);
+        in concatStringsSep "\n" outTunOpts))
+    (flip map
      (collect (tun: tun ? port && tun ? address) cfg.inTunnels)
-      (tun: ''
-        [${tun.name}]
-        type = server
-        destination = ${tun.destination}
-        keys = ${tun.keys}
-        host = ${tun.address}
-        port = ${toString tun.port}
-        inport = ${toString tun.inPort}
-        accesslist = ${builtins.concatStringsSep "," tun.accessList}
-      '')
-    }
-  '';
+      (tun: let inTunOpts = [
+        (sec tun.name)
+        "type = server"
+        (intOpt "port" tun.port)
+        (strOpt "host" tun.address)
+      ] ++ (if tun ? destination then
+            optionalNullString "destination" tun.destination else [])
+        ++ (if tun ? keys then
+            optionalNullString "keys" tun.keys else [])
+        ++ (if tun ? inPort then
+            optionalNullInt "inport" tun.inPort else [])
+        ++ (if tun ? accessList then
+            optionalEmptyList "accesslist" tun.accessList else []);
+        in concatStringsSep "\n" inTunOpts))];
+    in pkgs.writeText "i2pd-tunnels.conf" opts;

  i2pdSh = pkgs.writeScriptBin "i2pd" ''
    #!/bin/sh
    exec ${pkgs.i2pd}/bin/i2pd \
      ${if isNull cfg.address then "" else "--host="+cfg.address} \
+      --service \
      --conf=${i2pdConf} \
-      --tunconf=${i2pdTunnelConf}
+      --tunconf=${tunnelConf}
  '';

 in
@ -170,9 +241,7 @@ in

    services.i2pd = {

-      enable = mkOption {
-        type = types.bool;
-        default = false;
+      enable = mkEnableOption "I2Pd daemon" // {
        description = ''
          Enables I2Pd as a running service upon activation.
          Please read http://i2pd.readthedocs.io/en/latest/ for further
@ -192,6 +261,8 @@ in
        '';
      };

+      logCLFTime = mkEnableOption "Full CLF-formatted date and time to log";
+
      address = mkOption {
        type = with types; nullOr str;
        default = null;
@ -200,17 +271,72 @@ in
        '';
      };

-      notransit = mkOption {
-        type = types.bool;
-        default = false;
+      family = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          Specify a family the router belongs to.
+        '';
+      };
+
+      dataDir = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          Alternative path to storage of i2pd data (RI, keys, peer profiles, ...)
+        '';
+      };
+
+      share = mkOption {
+        type = types.int;
+        default = 100;
+        description = ''
+          Limit of transit traffic from max bandwidth in percents.
+        '';
+      };
+
+      ifname = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          Network interface to bind to.
+        '';
+      };
+
+      ifname4 = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          IPv4 interface to bind to.
+        '';
+      };
+
+      ifname6 = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          IPv6 interface to bind to.
+        '';
+      };
+
+      ntcpProxy = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          Proxy URL for NTCP transport.
+        '';
+      };
+
+      ntcp = mkEnableTrueOption "ntcp";
+      ssu = mkEnableTrueOption "ssu";
+
+      notransit = mkEnableOption "notransit" // {
        description = ''
          Tells the router to not accept transit tunnels during startup.
        '';
      };

-      floodfill = mkOption {
-        type = types.bool;
-        default = false;
+      floodfill = mkEnableOption "floodfill" // {
        description = ''
          If the router is declared to be unreachable and needs introduction nodes.
        '';
@ -241,51 +367,20 @@ in
        '';
      };

-      enableIPv4 = mkOption {
-        type = types.bool;
-        default = true;
+      enableIPv4 = mkEnableTrueOption "IPv4 connectivity";
+      enableIPv6 = mkEnableOption "IPv6 connectivity";
+      nat = mkEnableTrueOption "NAT bypass";
+
+      upnp.enable = mkEnableOption "UPnP service discovery";
+      upnp.name = mkOption {
+        type = types.str;
+        default = "I2Pd";
        description = ''
-          Enables IPv4 connectivity. Enabled by default.
+          Name i2pd appears in UPnP forwardings list.
        '';
      };

-      enableIPv6 = mkOption {
-        type = types.bool;
-        default = false;
-        description = ''
-          Enables IPv6 connectivity. Disabled by default.
-        '';
-      };
-
-      nat = mkOption {
-        type = types.bool;
-        default = true;
-        description = ''
-          Assume router is NATed. Enabled by default.
-        '';
-      };
-
-      upnp = {
-        enable = mkOption {
-          type = types.bool;
-          default = false;
-          description = ''
-            Enables UPnP.
-          '';
-        };
-
-        name = mkOption {
-          type = types.str;
-          default = "I2Pd";
-          description = ''
-            Name i2pd appears in UPnP forwardings list.
-          '';
-        };
-      };
-
-      precomputation.elgamal = mkOption {
-        type = types.bool;
-        default = true;
+      precomputation.elgamal = mkEnableTrueOption "Precomputed ElGamal tables" // {
        description = ''
          Whenever to use precomputated tables for ElGamal.
          <command>i2pd</command> defaults to <literal>false</literal>
@ -296,76 +391,154 @@ in
        '';
      };

-      reseed = {
-        verify = mkOption {
-          type = types.bool;
-          default = false;
-          description = ''
-            Request SU3 signature verification
-          '';
-        };
+      reseed.verify = mkEnableOption "SU3 signature verification";

-        file = mkOption {
-          type = types.str;
-          default = "";
-          description = ''
-            Full path to SU3 file to reseed from
-          '';
-        };
-
-        urls = mkOption {
-          type = with types; listOf str;
-          default = [
-            "https://reseed.i2p-project.de/"
-            "https://i2p.mooo.com/netDb/"
-            "https://netdb.i2p2.no/"
-            "https://us.reseed.i2p2.no:444/"
-            "https://uk.reseed.i2p2.no:444/"
-            "https://i2p.manas.ca:8443/"
-          ];
-          description = ''
-            Reseed URLs
-          '';
-        };
+      reseed.file = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          Full path to SU3 file to reseed from.
+        '';
      };

-      addressbook = {
-       defaulturl = mkOption {
-          type = types.str;
-          default = "http://joajgazyztfssty4w2on5oaqksz6tqoxbduy553y34mf4byv6gpq.b32.i2p/export/alive-hosts.txt";
-          description = ''
-            AddressBook subscription URL for initial setup
-          '';
-        };
-       subscriptions = mkOption {
-          type = with types; listOf str;
-          default = [
-            "http://inr.i2p/export/alive-hosts.txt"
-            "http://i2p-projekt.i2p/hosts.txt"
-            "http://stats.i2p/cgi-bin/newhosts.txt"
-          ];
-          description = ''
-            AddressBook subscription URLs
-          '';
-        };
+      reseed.urls = mkOption {
+        type = with types; listOf str;
+        default = [];
+        description = ''
+          Reseed URLs.
+        '';
+      };
+
+      reseed.floodfill = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          Path to router info of floodfill to reseed from.
+        '';
+      };
+
+      reseed.zipfile = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          Path to local .zip file to reseed from.
+        '';
+      };
+
+      reseed.proxy = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          URL for reseed proxy, supports http/socks.
+        '';
+      };
+
+     addressbook.defaulturl = mkOption {
+        type = types.str;
+        default = "http://joajgazyztfssty4w2on5oaqksz6tqoxbduy553y34mf4byv6gpq.b32.i2p/export/alive-hosts.txt";
+        description = ''
+          AddressBook subscription URL for initial setup
+        '';
+      };
+     addressbook.subscriptions = mkOption {
+        type = with types; listOf str;
+        default = [
+          "http://inr.i2p/export/alive-hosts.txt"
+          "http://i2p-projekt.i2p/hosts.txt"
+          "http://stats.i2p/cgi-bin/newhosts.txt"
+        ];
+        description = ''
+          AddressBook subscription URLs
+        '';
+      };
+
+      trust.enable = mkEnableOption "Explicit trust options";
+
+      trust.family = mkOption {
+        type = with types; nullOr str;
+        default = null;
+        description = ''
+          Router Familiy to trust for first hops.
+        '';
+      };
+
+      trust.routers = mkOption {
+        type = with types; listOf str;
+        default = [];
+        description = ''
+          Only connect to the listed routers.
+        '';
+      };
+
+      trust.hidden = mkEnableOption "Router concealment.";
+
+      websocket = mkEndpointOpt "websockets" "127.0.0.1" 7666;
+
+      exploratory.inbound = i2cpOpts "exploratory";
+      exploratory.outbound = i2cpOpts "exploratory";
+
+      ntcp2.enable = mkEnableTrueOption "NTCP2.";
+      ntcp2.published = mkEnableOption "NTCP2 publication.";
+      ntcp2.port = mkOption {
+        type = types.int;
+        default = 0;
+        description = ''
+          Port to listen for incoming NTCP2 connections (0=auto).
+        '';
      };

      limits.transittunnels = mkOption {
        type = types.int;
        default = 2500;
        description = ''
-          Maximum number of active transit sessions
+          Maximum number of active transit sessions.
+        '';
+      };
+
+      limits.coreSize = mkOption {
+        type = types.int;
+        default = 0;
+        description = ''
+          Maximum size of corefile in Kb (0 - use system limit).
+        '';
+      };
+
+      limits.openFiles = mkOption {
+        type = types.int;
+        default = 0;
+        description = ''
+          Maximum number of open files (0 - use system default).
+        '';
+      };
+
+      limits.ntcpHard = mkOption {
+        type = types.int;
+        default = 0;
+        description = ''
+          Maximum number of active transit sessions.
+        '';
+      };
+
+      limits.ntcpSoft = mkOption {
+        type = types.int;
+        default = 0;
+        description = ''
+          Threshold to start probabalistic backoff with ntcp sessions (default: use system limit).
+        '';
+      };
+
+      limits.ntcpThreads = mkOption {
+        type = types.int;
+        default = 1;
+        description = ''
+          Maximum number of threads used by NTCP DH worker.
        '';
      };

      proto.http = (mkEndpointOpt "http" "127.0.0.1" 7070) // {
-        auth = mkOption {
-          type = types.bool;
-          default = false;
-          description = ''
-            Enable authentication for webconsole.
-          '';
-        };
+
+        auth = mkEnableOption "Webconsole authentication";
+
        user = mkOption {
          type = types.str;
          default = "i2pd";
@ -373,6 +546,7 @@ in
            Username for webconsole access
          '';
        };
+
        pass = mkOption {
          type = types.str;
          default = "i2pd";
@ -380,11 +554,35 @@ in
            Password for webconsole access.
          '';
        };
+
+        strictHeaders = mkOption {
+          type = with types; nullOr bool;
+          default = null;
+          description = ''
+            Enable strict host checking on WebUI.
+          '';
+        };
+
+        hostname = mkOption {
+          type = with types; nullOr str;
+          default = null;
+          description = ''
+            Expected hostname for WebUI.
+          '';
+        };
      };

-      proto.httpProxy = mkKeyedEndpointOpt "httpproxy" "127.0.0.1" 4444 "";
-      proto.socksProxy = (mkKeyedEndpointOpt "socksproxy" "127.0.0.1" 4447 "")
+      proto.httpProxy = (mkKeyedEndpointOpt "httpproxy" "127.0.0.1" 4444 "httpproxy-keys.dat")
      // {
+        outproxy = mkOption {
+          type = with types; nullOr str;
+          default = null;
+          description = "Upstream outproxy bind address.";
+        };
+      };
+      proto.socksProxy = (mkKeyedEndpointOpt "socksproxy" "127.0.0.1" 4447 "socksproxy-keys.dat")
+      // {
+        outproxyEnable = mkEnableOption "SOCKS outproxy";
        outproxy = mkOption {
          type = types.str;
          default = "127.0.0.1";
@ -408,8 +606,8 @@ in
          { name, ... }: {
            options = {
              destinationPort = mkOption {
-                type = types.int;
-                default = 0;
+                type = with types; nullOr int;
+                default = null;
                description = "Connect to particular port at destination.";
              };
            } // commonTunOpts name;
--- a/nixos/modules/services/networking/iperf3.nix
+++ b/nixos/modules/services/networking/iperf3.nix
@ -0,0 +1,87 @@
+{ config, lib, pkgs, ... }: with lib;
+let
+  cfg = config.services.iperf3;
+
+  api = {
+    enable = mkEnableOption "iperf3 network throughput testing server";
+    port = mkOption {
+      type        = types.ints.u16;
+      default     = 5201;
+      description = "Server port to listen on for iperf3 client requsts.";
+    };
+    affinity = mkOption {
+      type        = types.nullOr types.ints.unsigned;
+      default     = null;
+      description = "CPU affinity for the process.";
+    };
+    bind = mkOption {
+      type        = types.nullOr types.str;
+      default     = null;
+      description = "Bind to the specific interface associated with the given address.";
+    };
+    verbose = mkOption {
+      type        = types.bool;
+      default     = false;
+      description = "Give more detailed output.";
+    };
+    forceFlush = mkOption {
+      type        = types.bool;
+      default     = false;
+      description = "Force flushing output at every interval.";
+    };
+    debug = mkOption {
+      type        = types.bool;
+      default     = false;
+      description = "Emit debugging output.";
+    };
+    rsaPrivateKey = mkOption {
+      type        = types.nullOr types.path;
+      default     = null;
+      description = "Path to the RSA private key (not password-protected) used to decrypt authentication credentials from the client.";
+    };
+    authorizedUsersFile = mkOption {
+      type        = types.nullOr types.path;
+      default     = null;
+      description = "Path to the configuration file containing authorized users credentials to run iperf tests.";
+    };
+    extraFlags = mkOption {
+      type        = types.listOf types.str;
+      default     = [ ];
+      description = "Extra flags to pass to iperf3(1).";
+    };
+  };
+
+  imp = {
+    systemd.services.iperf3 = {
+      description = "iperf3 daemon";
+      unitConfig.Documentation = "man:iperf3(1) https://iperf.fr/iperf-doc.php";
+      wantedBy = [ "multi-user.target" ];
+      after = [ "network.target" ];
+
+      serviceConfig = {
+        Restart = "on-failure";
+        RestartSec = 2;
+        DynamicUser = true;
+        PrivateDevices = true;
+        CapabilityBoundingSet = "";
+        NoNewPrivileges = true;
+        ExecStart = ''
+          ${pkgs.iperf3}/bin/iperf \
+            --server \
+            --port ${toString cfg.port} \
+            ${optionalString (cfg.affinity != null) "--affinity ${toString cfg.affinity}"} \
+            ${optionalString (cfg.bind != null) "--bind ${cfg.bind}"} \
+            ${optionalString (cfg.rsaPrivateKey != null) "--rsa-private-key-path ${cfg.rsaPrivateKey}"} \
+            ${optionalString (cfg.authorizedUsersFile != null) "--authorized-users-path ${cfg.authorizedUsersFile}"} \
+            ${optionalString cfg.verbose "--verbose"} \
+            ${optionalString cfg.debug "--debug"} \
+            ${optionalString cfg.forceFlush "--forceflush"} \
+            ${escapeShellArgs cfg.extraFlags}
+        '';
+      };
+    };
+  };
+in {
+  options.services.iperf3 = api;
+  config = mkIf cfg.enable imp;
+}
--- a/nixos/modules/services/networking/networkmanager.nix
+++ b/nixos/modules/services/networking/networkmanager.nix
@ -406,25 +406,25 @@ in {
      { source = configFile;
        target = "NetworkManager/NetworkManager.conf";
      }
-      { source = "${networkmanager-openvpn}/etc/NetworkManager/VPN/nm-openvpn-service.name";
+      { source = "${networkmanager-openvpn}/lib/NetworkManager/VPN/nm-openvpn-service.name";
        target = "NetworkManager/VPN/nm-openvpn-service.name";
      }
-      { source = "${networkmanager-vpnc}/etc/NetworkManager/VPN/nm-vpnc-service.name";
+      { source = "${networkmanager-vpnc}/lib/NetworkManager/VPN/nm-vpnc-service.name";
        target = "NetworkManager/VPN/nm-vpnc-service.name";
      }
-      { source = "${networkmanager-openconnect}/etc/NetworkManager/VPN/nm-openconnect-service.name";
+      { source = "${networkmanager-openconnect}/lib/NetworkManager/VPN/nm-openconnect-service.name";
        target = "NetworkManager/VPN/nm-openconnect-service.name";
      }
-      { source = "${networkmanager-fortisslvpn}/etc/NetworkManager/VPN/nm-fortisslvpn-service.name";
+      { source = "${networkmanager-fortisslvpn}/lib/NetworkManager/VPN/nm-fortisslvpn-service.name";
        target = "NetworkManager/VPN/nm-fortisslvpn-service.name";
      }
-      { source = "${networkmanager-l2tp}/etc/NetworkManager/VPN/nm-l2tp-service.name";
+      { source = "${networkmanager-l2tp}/lib/NetworkManager/VPN/nm-l2tp-service.name";
        target = "NetworkManager/VPN/nm-l2tp-service.name";
      }
-      { source = "${networkmanager_strongswan}/etc/NetworkManager/VPN/nm-strongswan-service.name";
+      { source = "${networkmanager_strongswan}/lib/NetworkManager/VPN/nm-strongswan-service.name";
        target = "NetworkManager/VPN/nm-strongswan-service.name";
      }
-      { source = "${networkmanager-iodine}/etc/NetworkManager/VPN/nm-iodine-service.name";
+      { source = "${networkmanager-iodine}/lib/NetworkManager/VPN/nm-iodine-service.name";
        target = "NetworkManager/VPN/nm-iodine-service.name";
      }
    ] ++ optional (cfg.appendNameservers == [] || cfg.insertNameservers == [])
--- a/nixos/modules/services/security/sks.nix
+++ b/nixos/modules/services/security/sks.nix
@ -3,78 +3,112 @@
 with lib;

 let
-
  cfg = config.services.sks;
-
  sksPkg = cfg.package;

-in
-
-{
+in {
+  meta.maintainers = with maintainers; [ primeos calbrecht jcumming ];

  options = {

    services.sks = {

-      enable = mkEnableOption "sks";
+      enable = mkEnableOption ''
+        SKS (synchronizing key server for OpenPGP) and start the database
+        server. You need to create "''${dataDir}/dump/*.gpg" for the initial
+        import'';

      package = mkOption {
        default = pkgs.sks;
        defaultText = "pkgs.sks";
        type = types.package;
-        description = "
-          Which sks derivation to use.
-        ";
+        description = "Which SKS derivation to use.";
+      };
+
+      dataDir = mkOption {
+        type = types.path;
+        default = "/var/db/sks";
+        example = "/var/lib/sks";
+        # TODO: The default might change to "/var/lib/sks" as this is more
+        # common. There's also https://github.com/NixOS/nixpkgs/issues/26256
+        # and "/var/db" is not FHS compliant (seems to come from BSD).
+        description = ''
+          Data directory (-basedir) for SKS, where the database and all
+          configuration files are located (e.g. KDB, PTree, membership and
+          sksconf).
+        '';
      };

      hkpAddress = mkOption {
        default = [ "127.0.0.1" "::1" ];
        type = types.listOf types.str;
-        description = "
-          Wich ip addresses the sks-keyserver is listening on.
-        ";
+        description = ''
+          Domain names, IPv4 and/or IPv6 addresses to listen on for HKP
+          requests.
+        '';
      };

      hkpPort = mkOption {
        default = 11371;
-        type = types.int;
-        description = "
-          Which port the sks-keyserver is listening on.
-        ";
+        type = types.ints.u16;
+        description = "HKP port to listen on.";
+      };
+
+      webroot = mkOption {
+        type = types.nullOr types.path;
+        default = "${sksPkg.webSamples}/OpenPKG";
+        defaultText = "\${pkgs.sks.webSamples}/OpenPKG";
+        description = ''
+          Source directory (will be symlinked, if not null) for the files the
+          built-in webserver should serve. SKS (''${pkgs.sks.webSamples})
+          provides the following examples: "HTML5", "OpenPKG", and "XHTML+ES".
+          The index file can be named index.html, index.htm, index.xhtm, or
+          index.xhtml. Files with the extensions .css, .es, .js, .jpg, .jpeg,
+          .png, or .gif are supported. Subdirectories and filenames with
+          anything other than alphanumeric characters and the '.' character
+          will be ignored.
+        '';
      };
    };
  };

  config = mkIf cfg.enable {

-    environment.systemPackages = [ sksPkg ];
-    
-    users.users.sks = {
-      createHome = true;
-      home = "/var/db/sks";
-      isSystemUser = true;
-      shell = "${pkgs.coreutils}/bin/true";
+    users = {
+      users.sks = {
+        isSystemUser = true;
+        description = "SKS user";
+        home = cfg.dataDir;
+        createHome = true;
+        group = "sks";
+        useDefaultShell = true;
+        packages = [ sksPkg pkgs.db ];
+      };
+      groups.sks = { };
    };

    systemd.services = let
      hkpAddress = "'" + (builtins.concatStringsSep " " cfg.hkpAddress) + "'" ;
      hkpPort = builtins.toString cfg.hkpPort;
-      home = config.users.users.sks.home;
-      user = config.users.users.sks.name;
    in {
-      sks-keyserver = {
+      "sks-db" = {
+        description = "SKS database server";
+        after = [ "network.target" ];
        wantedBy = [ "multi-user.target" ];
        preStart = ''
-          mkdir -p ${home}/dump
-          ${pkgs.sks}/bin/sks build ${home}/dump/*.gpg -n 10 -cache 100 || true #*/
-          ${pkgs.sks}/bin/sks cleandb || true
-          ${pkgs.sks}/bin/sks pbuild -cache 20 -ptree_cache 70 || true
+          ${lib.optionalString (cfg.webroot != null)
+            "ln -sfT \"${cfg.webroot}\" web"}
+          mkdir -p dump
+          ${sksPkg}/bin/sks build dump/*.gpg -n 10 -cache 100 || true #*/
+          ${sksPkg}/bin/sks cleandb || true
+          ${sksPkg}/bin/sks pbuild -cache 20 -ptree_cache 70 || true
        '';
        serviceConfig = {
-          WorkingDirectory = home;
-          User = user;
+          WorkingDirectory = "~";
+          User = "sks";
+          Group = "sks";
          Restart = "always";
-          ExecStart = "${pkgs.sks}/bin/sks db -hkp_address ${hkpAddress} -hkp_port ${hkpPort}";
+          ExecStart = "${sksPkg}/bin/sks db -hkp_address ${hkpAddress} -hkp_port ${hkpPort}";
        };
      };
    };
--- a/nixos/modules/services/x11/desktop-managers/enlightenment.nix
+++ b/nixos/modules/services/x11/desktop-managers/enlightenment.nix
@ -66,7 +66,7 @@ in
      '';
    }];

-    security.wrappers = (import (builtins.toPath "${e.enlightenment}/e-wrappers.nix")).security.wrappers;
+    security.wrappers = (import "${e.enlightenment}/e-wrappers.nix").security.wrappers;

    environment.etc = singleton
      { source = xcfg.xkbDir;
--- a/nixos/modules/services/x11/desktop-managers/gnome3.nix
+++ b/nixos/modules/services/x11/desktop-managers/gnome3.nix
@ -110,6 +110,7 @@ in {
    services.gnome3.gnome-terminal-server.enable = mkDefault true;
    services.gnome3.gnome-user-share.enable = mkDefault true;
    services.gnome3.gvfs.enable = true;
+    services.gnome3.rygel.enable = mkDefault true;
    services.gnome3.seahorse.enable = mkDefault true;
    services.gnome3.sushi.enable = mkDefault true;
    services.gnome3.tracker.enable = mkDefault true;
--- a/nixos/modules/system/boot/networkd.nix
+++ b/nixos/modules/system/boot/networkd.nix
@ -208,7 +208,6 @@ let
      "InitialCongestionWindow" "InitialAdvertisedReceiveWindow" "QuickAck"
      "MTUBytes"
    ])
-    (assertHasField "Gateway")
  ];

  checkDhcp = checkUnitConfig "DHCP" [
@ -249,13 +248,14 @@ let
  # .network files have a [Link] section with different options than in .netlink files
  checkNetworkLink = checkUnitConfig "Link" [
    (assertOnlyFields [
-      "MACAddress" "MTUBytes" "ARP" "Unmanaged" "RequiredForOnline"
+      "MACAddress" "MTUBytes" "ARP" "Multicast" "Unmanaged" "RequiredForOnline"
    ])
    (assertMacAddress "MACAddress")
    (assertByteFormat "MTUBytes")
    (assertValueOneOf "ARP" boolValues)
+    (assertValueOneOf "Multicast" boolValues)
    (assertValueOneOf "Unmanaged" boolValues)
-    (assertValueOneOf "RquiredForOnline" boolValues)
+    (assertValueOneOf "RequiredForOnline" boolValues)
  ];


--- a/pkgs/applications/altcoins/btc1.nix
+++ b/pkgs/applications/altcoins/btc1.nix
@ -1,6 +1,8 @@
-{ stdenv, fetchurl, pkgconfig, autoreconfHook, openssl, db48, boost
-, zlib, miniupnpc, qt4, utillinux, protobuf, qrencode, libevent
-, withGui }:
+{ stdenv, fetchurl, pkgconfig, autoreconfHook, hexdump, openssl, db48
+, boost, zlib, miniupnpc, qt4, utillinux, protobuf, qrencode, libevent
+, AppKit
+, withGui ? !stdenv.isDarwin
+}:

 with stdenv.lib;
 stdenv.mkDerivation rec{
@ -12,11 +14,10 @@ stdenv.mkDerivation rec{
    sha256 = "0v0g2wb4nsnhddxzb63vj2bc1mgyj05vqm5imicjfz8prvgc0si8";
  };

-  nativeBuildInputs = [ pkgconfig autoreconfHook ];
-  buildInputs = [ openssl db48 boost zlib
-                  miniupnpc protobuf libevent]
-                  ++ optionals stdenv.isLinux [ utillinux ]
-                  ++ optionals withGui [ qt4 qrencode ];
+  nativeBuildInputs = [ pkgconfig autoreconfHook hexdump ];
+  buildInputs = [ openssl db48 boost zlib miniupnpc protobuf libevent ]
+    ++ optionals withGui [ qt4 qrencode ]
+    ++ optional stdenv.isDarwin AppKit;

  configureFlags = [ "--with-boost-libdir=${boost.out}/lib" ]
                     ++ optionals withGui [ "--with-gui=qt4" ];
--- a/pkgs/applications/altcoins/default.nix
+++ b/pkgs/applications/altcoins/default.nix
@ -32,8 +32,11 @@ rec {
    boost = boost165; withGui = false;
  };

-  btc1 = callPackage ./btc1.nix { boost = boost165; withGui = true; };
-  btc1d = callPackage ./btc1.nix { boost = boost165; withGui = false; };
+  btc1 = callPackage ./btc1.nix {
+    inherit (darwin.apple_sdk.frameworks) AppKit;
+    boost = boost165;
+  };
+  btc1d = btc1.override { withGui = false; };

  cryptop = python3.pkgs.callPackage ./cryptop { };

--- a/pkgs/applications/audio/pulseaudio-modules-bt/default.nix
+++ b/pkgs/applications/audio/pulseaudio-modules-bt/default.nix
@ -0,0 +1,63 @@
+{ stdenv
+, runCommand
+, fetchFromGitHub
+, libpulseaudio
+, pulseaudio
+, pkgconfig
+, libtool
+, cmake
+, bluez
+, dbus
+, sbc
+}:
+
+let
+  pulseSources = runCommand "pulseaudio-sources" {} ''
+    mkdir $out
+    tar -xf ${pulseaudio.src}
+    mv pulseaudio*/* $out/
+  '';
+
+in stdenv.mkDerivation rec {
+  name = "pulseaudio-modules-bt-${version}";
+  version = "unstable-2018-09-11";
+
+  src = fetchFromGitHub {
+    owner = "EHfive";
+    repo = "pulseaudio-modules-bt";
+    rev = "9c6ad75382f3855916ad2feaa6b40e37356d80cc";
+    sha256 = "1iz4m3y6arsvwcyvqc429w252dl3apnhvl1zhyvfxlbg00d2ii0h";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [
+    pkgconfig
+    cmake
+  ];
+
+  buildInputs = [
+    libpulseaudio
+    pulseaudio
+    libtool
+    bluez
+    dbus
+    sbc
+  ];
+
+  NIX_CFLAGS_COMPILE = [
+    "-L${pulseaudio}/lib/pulseaudio"
+  ];
+
+  prePatch = ''
+    rm -r pa
+    ln -s ${pulseSources} pa
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/EHfive/pulseaudio-modules-bt;
+    description = "SBC, Sony LDAC codec (A2DP Audio) support for Pulseaudio";
+    platforms = platforms.linux;
+    license = licenses.mit;
+    maintainers = with maintainers; [ adisbladis ];
+  };
+}
--- a/pkgs/applications/audio/qmmp/default.nix
+++ b/pkgs/applications/audio/qmmp/default.nix
@ -29,11 +29,11 @@
 # handle that.

 stdenv.mkDerivation rec {
-  name = "qmmp-1.2.2";
+  name = "qmmp-1.2.3";

  src = fetchurl {
    url = "http://qmmp.ylsoftware.com/files/${name}.tar.bz2";
-    sha256 = "01nnyg8m3p3px1fj3lfsqqv9zh1388dwx1bm2qv4v87jywimgp79";
+    sha256 = "05lqmj22vr5ch1i0928d64ybdnn3qc66s9lgarx5s6x6ffr6589j";
  };

  buildInputs =
--- a/pkgs/applications/editors/android-studio/default.nix
+++ b/pkgs/applications/editors/android-studio/default.nix
@ -13,9 +13,9 @@ let
    sha256Hash = "0xx6yprylmcb32ipmwdcfkgddlm1nrxi1w68miclvgrbk015brf2";
  };
  betaVersion = {
-    version = "3.2.0.24"; # "Android Studio 3.2 RC 2"
-    build = "181.4974118";
-    sha256Hash = "0sj848pzpsbmnfi2692gg73v6m72hr1pwlk5x8q912w60iypi3pz";
+    version = "3.2.0.25"; # "Android Studio 3.2 RC 3"
+    build = "181.4987877";
+    sha256Hash = "0mriakxxchc0wbqkl236pp4fsqbq3gb2qrkdg5hx9zz763dc59gp";
  };
  latestVersion = { # canary & dev
    version = "3.3.0.7"; # "Android Studio 3.3 Canary 8"
--- a/pkgs/applications/editors/aseprite/default.nix
+++ b/pkgs/applications/editors/aseprite/default.nix
@ -1,5 +1,5 @@
-{ stdenv, lib, fetchFromGitHub, cmake, pkgconfig
-, curl, freetype, giflib, libjpeg, libpng, libwebp, pixman, tinyxml, zlib
+{ stdenv, lib, fetchFromGitHub, fetchpatch, cmake, pkgconfig
+, curl, freetype, giflib, harfbuzz, libjpeg, libpng, libwebp, pixman, tinyxml, zlib
 , libX11, libXext, libXcursor, libXxf86vm
 , unfree ? false
 , cmark
@ -11,7 +11,7 @@

 stdenv.mkDerivation rec {
  name = "aseprite-${version}";
-  version = if unfree then "1.2.4" else "1.1.7";
+  version = if unfree then "1.2.9" else "1.1.7";

  src = fetchFromGitHub {
    owner = "aseprite";
@ -19,16 +19,27 @@ stdenv.mkDerivation rec {
    rev = "v${version}";
    fetchSubmodules = true;
    sha256 = if unfree
-      then "1rnf4a8vgddz8x55rpqaihlxmqip1kgpdhqb4d3l71h1zmidg5k3"
+      then "0a9xk163j0984n8nn6pqf27n83gr6w7g25wkiv591zx88pa6cpbd"
      else "0gd49lns2bpzbkwax5jf9x1xmg1j8ij997kcxr2596cwiswnw4di";
  };

  nativeBuildInputs = [ cmake pkgconfig ];

  buildInputs = [
-    curl freetype giflib libjpeg libpng libwebp pixman tinyxml zlib
+    curl freetype giflib harfbuzz libjpeg libpng libwebp pixman tinyxml zlib
    libX11 libXext libXcursor libXxf86vm
-  ] ++ lib.optionals unfree [ cmark ];
+  ] ++ lib.optionals unfree [ cmark harfbuzz ];
+
+  patches = lib.optionals unfree [
+    (fetchpatch {
+      url = "https://github.com/aseprite/aseprite/commit/cfb4dac6feef1f39e161c23c886055a8f9acfd0d.patch";
+      sha256 = "1qhjfpngg8b1vvb9w26lhjjfamfx57ih0p31km3r5l96nm85l7f9";
+    })
+    (fetchpatch {
+      url = "https://github.com/orivej/aseprite/commit/ea87e65b357ad0bd65467af5529183b5a48a8c17.patch";
+      sha256 = "1vwn8ivap1pzdh444sdvvkndp55iz146nhmd80xbm8cyzn3qmg91";
+    })
+  ];

  postPatch = ''
    sed -i src/config.h -e "s-\\(#define VERSION\\) .*-\\1 \"$version\"-"
@ -49,6 +60,7 @@ stdenv.mkDerivation rec {
    "-DWITH_WEBP_SUPPORT=ON"
  ] ++ lib.optionals unfree [
    "-DUSE_SHARED_CMARK=ON"
+    "-DUSE_SHARED_HARFBUZZ=ON"
    # Aseprite needs internal freetype headers.
    "-DUSE_SHARED_FREETYPE=OFF"
    # Disable libarchive programs.
--- a/pkgs/applications/editors/emacs/default.nix
+++ b/pkgs/applications/editors/emacs/default.nix
@ -4,8 +4,9 @@
 , alsaLib, cairo, acl, gpm, AppKit, GSS, ImageIO, m17n_lib, libotf
 , systemd ? null
 , withX ? !stdenv.isDarwin
-, withGTK2 ? false, gtk2 ? null
-, withGTK3 ? true, gtk3 ? null, gsettings-desktop-schemas ? null
+, withNS ? stdenv.isDarwin
+, withGTK2 ? false, gtk2-x11 ? null
+, withGTK3 ? true, gtk3-x11 ? null, gsettings-desktop-schemas ? null
 , withXwidgets ? false, webkitgtk ? null, wrapGAppsHook ? null, glib-networking ? null
 , withCsrc ? true
 , srcRepo ? false, autoconf ? null, automake ? null, texinfo ? null
@ -13,10 +14,12 @@

 assert (libXft != null) -> libpng != null;      # probably a bug
 assert stdenv.isDarwin -> libXaw != null;       # fails to link otherwise
-assert withGTK2 -> withX || stdenv.isDarwin;
-assert withGTK3 -> withX || stdenv.isDarwin;
-assert withGTK2 -> !withGTK3 && gtk2 != null;
-assert withGTK3 -> !withGTK2 && gtk3 != null;
+assert withNS -> !withX;
+assert withNS -> stdenv.isDarwin;
+assert (withGTK2 && !withNS) -> withX;
+assert (withGTK3 && !withNS) -> withX;
+assert withGTK2 -> !withGTK3 && gtk2-x11 != null;
+assert withGTK3 -> !withGTK2 && gtk3-x11 != null;
 assert withXwidgets -> withGTK3 && webkitgtk != null;

 let
@ -56,19 +59,22 @@ stdenv.mkDerivation rec {
    ++ lib.optionals stdenv.isLinux [ dbus libselinux systemd ]
    ++ lib.optionals withX
      [ xlibsWrapper libXaw Xaw3d libXpm libpng libjpeg libungif libtiff librsvg libXft
-        imagemagick gconf m17n_lib libotf ]
-    ++ lib.optional (withX && withGTK2) gtk2
-    ++ lib.optionals (withX && withGTK3) [ gtk3 gsettings-desktop-schemas ]
+        imagemagick gconf ]
+    ++ lib.optionals (stdenv.isLinux && withX) [ m17n_lib libotf ]
+    ++ lib.optional (withX && withGTK2) gtk2-x11
+    ++ lib.optionals (withX && withGTK3) [ gtk3-x11 gsettings-desktop-schemas ]
    ++ lib.optional (stdenv.isDarwin && withX) cairo
    ++ lib.optionals (withX && withXwidgets) [ webkitgtk ];

-  propagatedBuildInputs = lib.optionals stdenv.isDarwin [ AppKit GSS ImageIO ];
+  propagatedBuildInputs = lib.optionals withNS [ AppKit GSS ImageIO ];

  hardeningDisable = [ "format" ];

  configureFlags = [ "--with-modules" ] ++
-   (if stdenv.isDarwin
-      then [ "--with-ns" "--disable-ns-self-contained" ]
+    (lib.optional stdenv.isDarwin
+      (lib.withFeature withNS "ns")) ++
+    (if withNS
+      then [ "--disable-ns-self-contained" ]
    else if withX
      then [ "--with-x-toolkit=${toolkit}" "--with-xft" ]
      else [ "--with-x=no" "--with-xpm=no" "--with-jpeg=no" "--with-png=no"
@ -103,7 +109,7 @@ stdenv.mkDerivation rec {
      cp $srcdir/TAGS $dstdir
      echo '((nil . ((tags-file-name . "TAGS"))))' > $dstdir/.dir-locals.el
    done
-  '' + lib.optionalString stdenv.isDarwin ''
+  '' + lib.optionalString withNS ''
    mkdir -p $out/Applications
    mv nextstep/Emacs.app $out/Applications
  '';
--- a/pkgs/applications/editors/nano/default.nix
+++ b/pkgs/applications/editors/nano/default.nix
@ -14,17 +14,17 @@ let
  nixSyntaxHighlight = fetchFromGitHub {
    owner = "seitz";
    repo = "nanonix";
-    rev = "7483fd8b79f1f3f2179dbbd46aa400df4320ba10";
-    sha256 = "10pv75kfrgnziz8sr83hdbb0c3klm2fmsdw3i5cpqqf5va1fzb8h";
+    rev = "bf8d898efaa10dce3f7972ff765b58c353b4b4ab";
+    sha256 = "0773s5iz8aw9npgyasb0r2ybp6gvy2s9sq51az8w7h52bzn5blnn";
  };

 in stdenv.mkDerivation rec {
  name = "nano-${version}";
-  version = "2.9.8";
+  version = "3.0";

  src = fetchurl {
    url = "mirror://gnu/nano/${name}.tar.xz";
-    sha256 = "122lm0z97wk3mgnbn8m4d769d4j9rxyc9z7s89xd4gsdp8qsrpn2";
+    sha256 = "1868hg9s584fwjrh0fzdrixmxc2qhw520z4q5iv68kjiajivr9g0";
  };

  nativeBuildInputs = [ texinfo ] ++ optional enableNls gettext;
--- a/pkgs/applications/editors/nano/nanorc/default.nix
+++ b/pkgs/applications/editors/nano/nanorc/default.nix
@ -0,0 +1,29 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  name = "nanorc-${version}";
+  version = "2018-09-05";
+
+  src = fetchFromGitHub {
+    owner = "scopatz";
+    repo = "nanorc";
+    rev = "1e589cb729d24fba470228d429e6dde07973d597";
+    sha256 = "136yxr38lzrfv8bar0c6c56rh54q9s94zpwa19f425crh44drppl";
+  };
+
+  dontBuild = true;
+
+  installPhase = ''
+    mkdir -p $out/share
+
+    install *.nanorc $out/share/
+  '';
+
+  meta = {
+    description = "Improved Nano Syntax Highlighting Files";
+    homepage = https://github.com/scopatz/nanorc;
+    license = stdenv.lib.licenses.gpl3;
+    maintainers = with stdenv.lib.maintainers; [ nequissimus ];
+    platforms = stdenv.lib.platforms.all;
+  };
+}
--- a/pkgs/applications/editors/okteta/default.nix
+++ b/pkgs/applications/editors/okteta/default.nix
@ -4,11 +4,11 @@

 stdenv.mkDerivation rec {
  name = "okteta-${version}";
-  version = "0.25.2";
+  version = "0.25.3";

  src = fetchurl {
    url = "mirror://kde/stable/okteta/${version}/src/${name}.tar.xz";
-    sha256 = "00mw8gdqvn6vn6ir6kqnp7xi3lpn6iyp4f5aknxwq6mdcxgjmh1p";
+    sha256 = "0mm6pmk7k9c581b12a3wl0ayhadvyymfzmscy9x32b391qy9inai";
  };

  nativeBuildInputs = [ qtscript extra-cmake-modules kdoctools ];
--- a/pkgs/applications/editors/rednotebook/default.nix
+++ b/pkgs/applications/editors/rednotebook/default.nix
@ -5,13 +5,13 @@

 buildPythonApplication rec {
  pname = "rednotebook";
-  version = "2.3";
+  version = "2.6.1";

  src = fetchFromGitHub {
    owner = "jendrikseipp";
    repo = "rednotebook";
    rev = "v${version}";
-    sha256 = "0zkfid104hcsf20r6829v11wxdghqkd3j1zbgyvd1s7q4nxjn5lj";
+    sha256 = "1x6acx0hagsawx84cv55qz17p8qjpq1v1zaf8rmm6ifsslsxw91h";
  };

  # We have not packaged tests.
--- a/pkgs/applications/editors/thonny/default.nix
+++ b/pkgs/applications/editors/thonny/default.nix
@ -0,0 +1,43 @@
+{ stdenv, fetchFromBitbucket, python3 }:
+
+with python3.pkgs;
+
+buildPythonApplication rec {
+  pname = "thonny";
+  version = "3.0.0b3";
+
+  src = fetchFromBitbucket {
+    owner = "plas";
+    repo = pname;
+    rev = "a511d4539c532b6dddf6d7f1586d30e1ac35bd86";
+    sha256 = "1s3pp97r6p3j81idglnml4faxryk7saszxmv3gys1agdfj75qczr";
+  };
+
+  propagatedBuildInputs = with python3.pkgs; [ jedi pyserial tkinter docutils pylint ];
+
+  preInstall = ''
+    export HOME=$(mktemp -d)
+  '';
+
+  preFixup = ''
+    wrapProgram "$out/bin/thonny" \
+       --prefix PYTHONPATH : $PYTHONPATH:$(toPythonPath ${python3.pkgs.jedi})
+  '';
+
+  # Tests need a DISPLAY
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Python IDE for beginners";
+    longDescription = ''
+      Thonny is a Python IDE for beginners. It supports different ways
+      of stepping through the code, step-by-step expression
+      evaluation, detailed visualization of the call stack and a mode
+      for explaining the concepts of references and heap.
+    '';
+    homepage = https://www.thonny.org/;
+    license = licenses.mit;
+    maintainers = with maintainers; [ leenaars ];
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/graphics/PythonMagick/default.nix
+++ b/pkgs/applications/graphics/PythonMagick/default.nix
@ -1,6 +1,6 @@
 # This expression provides Python bindings to ImageMagick. Python libraries are supposed to be called via `python-packages.nix`.

-{stdenv, fetchurl, python, boost, pkgconfig, imagemagick}:
+{ stdenv, fetchurl, python, pkgconfig, imagemagick, autoreconfHook }:

 stdenv.mkDerivation rec {
  name = "pythonmagick-${version}";
@ -11,10 +11,18 @@ stdenv.mkDerivation rec {
    sha256 = "137278mfb5079lns2mmw73x8dhpzgwha53dyl00mmhj2z25varpn";
  };

-  nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [python boost imagemagick];
+  postPatch = ''
+    rm configure
+  '';

-  meta = {
+  configureFlags = [ "--with-boost=${python.pkgs.boost}" ];
+
+  nativeBuildInputs = [ pkgconfig autoreconfHook ];
+  buildInputs = [ python python.pkgs.boost imagemagick ];
+
+  meta = with stdenv.lib; {
    homepage = http://www.imagemagick.org/script/api.php;
+    license = licenses.imagemagick;
+    description = "PythonMagick provides object oriented bindings for the ImageMagick Library.";
  };
 }
--- a/pkgs/applications/graphics/antimony/default.nix
+++ b/pkgs/applications/graphics/antimony/default.nix
@ -1,29 +1,34 @@
-{ stdenv, fetchFromGitHub, libpng, python3, boost, libGLU_combined, qtbase, ncurses, cmake, flex, lemon }:
+{ stdenv, fetchFromGitHub, libpng, python3
+, libGLU_combined, qtbase, ncurses
+, cmake, flex, lemon
+}:

 let
-  gitRev    = "020910c25614a3752383511ede5a1f5551a8bd39";
-  gitBranch = "master";
+  gitRev    = "60a58688e552f12501980c4bdab034ab0f2ba059";
+  gitBranch = "develop";
  gitTag    = "0.9.3";
 in
  stdenv.mkDerivation rec {
    name    = "antimony-${version}";
-    version = gitTag;
+    version = "2018-07-17";

    src = fetchFromGitHub {
-      owner = "mkeeter";
-      repo = "antimony";
-      rev = gitTag;
-      sha256 = "1vm5h5py8l3b8h4pbmm8s3wlxvlw492xfwnlwx0nvl0cjs8ba6r4";
+      owner  = "mkeeter";
+      repo   = "antimony";
+      rev    = gitRev;
+      sha256 = "0pgf6kr23xw012xsil56j5gq78mlirmrlqdm09m5wlgcf4vr6xnl";
    };

    patches = [ ./paths-fix.patch ];

    postPatch = ''
-       sed -i "s,/usr/local,$out,g" app/CMakeLists.txt app/app/app.cpp app/app/main.cpp
+       sed -i "s,/usr/local,$out,g" \
+       app/CMakeLists.txt app/app/app.cpp app/app/main.cpp
+       sed -i "s,python-py35,python36," CMakeLists.txt
    '';

    buildInputs = [
-      libpng python3 (boost.override { python = python3; })
+      libpng python3 python3.pkgs.boost
      libGLU_combined qtbase ncurses
    ];

@ -41,6 +46,7 @@ in
      description = "A computer-aided design (CAD) tool from a parallel universe";
      homepage    = "https://github.com/mkeeter/antimony";
      license     = licenses.mit;
+      maintainers = with maintainers; [ rnhmjoj ];
      platforms   = platforms.linux;
    };
  }
--- a/pkgs/applications/graphics/imv/default.nix
+++ b/pkgs/applications/graphics/imv/default.nix
@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
    homepage    = https://github.com/eXeC64/imv; 
    license     = licenses.gpl2;
    maintainers = with maintainers; [ rnhmjoj ];
-    platforms   = [ "x86_64-linux" ];
+    platforms   = [ "i686-linux" "x86_64-linux" ];
  };
 }

--- a/pkgs/applications/graphics/kipi-plugins/default.nix
+++ b/pkgs/applications/graphics/kipi-plugins/default.nix
@ -7,11 +7,11 @@

 stdenv.mkDerivation rec {
  name    = "kipi-plugins-${version}";
-  version = "5.2.0";
+  version = "5.9.0";

  src = fetchurl {
    url = "http://download.kde.org/stable/digikam/digikam-${version}.tar.xz";
-    sha256 = "0q4j7iv20cxgfsr14qwzx05wbp2zkgc7cg2pi7ibcnwba70ky96g";
+    sha256 = "06qdalf2mwx2f43p3bljy3vn5bk8n3x539kha6ky2vzxvkp343b6";
  };

  prePatch = ''
--- a/pkgs/applications/kde/fetch.sh
+++ b/pkgs/applications/kde/fetch.sh
@ -1 +1 @@
-WGET_ARGS=( https://download.kde.org/stable/applications/18.08.0/ -A '*.tar.xz' )
+WGET_ARGS=( https://download.kde.org/stable/applications/18.08.1/ -A '*.tar.xz' )
--- a/pkgs/applications/kde/srcs.nix
+++ b/pkgs/applications/kde/srcs.nix
--- a/pkgs/applications/misc/dbeaver/default.nix
+++ b/pkgs/applications/misc/dbeaver/default.nix
@ -7,7 +7,7 @@

 stdenv.mkDerivation rec {
  name = "dbeaver-ce-${version}";
-  version = "5.1.6";
+  version = "5.2.0";

  desktopItem = makeDesktopItem {
    name = "dbeaver";
@ -30,7 +30,7 @@ stdenv.mkDerivation rec {

  src = fetchurl {
    url = "https://dbeaver.io/files/${version}/dbeaver-ce-${version}-linux.gtk.x86_64.tar.gz";
-    sha256 = "1zypadnyhinm6mfv91s7zs2s55bhzgkqhl6ai6x3yqwhvayc02nn";
+    sha256 = "13j2qc4g24d2gmkxj9zpqrcbai9aq8rassrq3c9mp9ir6sf4q0jf";
  };

  installPhase = ''
--- a/pkgs/applications/misc/josm/default.nix
+++ b/pkgs/applications/misc/josm/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  name = "josm-${version}";
-  version = "14066";
+  version = "14178";

  src = fetchurl {
    url = "https://josm.openstreetmap.de/download/josm-snapshot-${version}.jar";
-    sha256 = "06mhaz5vr19ydqc5irhgcbl0s8fifwvaq60iz2nsnlxb1pw89xia";
+    sha256 = "08an4s8vbcd8vyinnvd7cxmgnrsy47j78a94nk6vq244gp7v5n0r";
  };

  buildInputs = [ jre10 makeWrapper ];
--- a/pkgs/applications/misc/khal/default.nix
+++ b/pkgs/applications/misc/khal/default.nix
@ -46,6 +46,10 @@ in with python.pkgs; buildPythonApplication rec {
  nativeBuildInputs = [ setuptools_scm pkgs.glibcLocales ];
  checkInputs = [ pytest ];

+  postInstall = ''
+    install -D misc/__khal $out/share/zsh/site-functions/__khal
+  '';
+
  checkPhase = ''
    py.test
  '';
--- a/pkgs/applications/misc/lilyterm/default.nix
+++ b/pkgs/applications/misc/lilyterm/default.nix
@ -1,13 +1,12 @@
-{ stdenv, fetchurl, fetchFromGitHub
+{ stdenv, lib, fetchurl, fetchFromGitHub
 , pkgconfig
 , autoconf, automake, intltool, gettext
 , gtk, vte

-# "stable" or "git"
 , flavour ? "stable"
 }:

-assert flavour == "stable" || flavour == "git";
+assert lib.assertOneOf "flavour" flavour [ "stable"  "git" ];

 let
  stuff =
--- a/pkgs/applications/misc/mediainfo-gui/default.nix
+++ b/pkgs/applications/misc/mediainfo-gui/default.nix
@ -2,11 +2,11 @@
 , desktop-file-utils, libSM, imagemagick }:

 stdenv.mkDerivation rec {
-  version = "18.05";
+  version = "18.08";
  name = "mediainfo-gui-${version}";
  src = fetchurl {
    url = "https://mediaarea.net/download/source/mediainfo/${version}/mediainfo_${version}.tar.xz";
-    sha256 = "0rgsfplisf729n1j3fyg82wpw88aahisrddn5wq9yx8hz6m96h6r";
+    sha256 = "0l4bhrgwfn3da6cr0jz5vs17sk7k0bc26nk7hymv04xifns5999n";
  };

  nativeBuildInputs = [ autoreconfHook pkgconfig ];
--- a/pkgs/applications/misc/mediainfo/default.nix
+++ b/pkgs/applications/misc/mediainfo/default.nix
@ -1,11 +1,11 @@
 { stdenv, fetchurl, autoreconfHook, pkgconfig, libzen, libmediainfo, zlib }:

 stdenv.mkDerivation rec {
-  version = "18.05";
+  version = "18.08";
  name = "mediainfo-${version}";
  src = fetchurl {
    url = "https://mediaarea.net/download/source/mediainfo/${version}/mediainfo_${version}.tar.xz";
-    sha256 = "0rgsfplisf729n1j3fyg82wpw88aahisrddn5wq9yx8hz6m96h6r";
+    sha256 = "0l4bhrgwfn3da6cr0jz5vs17sk7k0bc26nk7hymv04xifns5999n";
  };

  nativeBuildInputs = [ autoreconfHook pkgconfig ];
--- a/pkgs/applications/misc/ranger/default.nix
+++ b/pkgs/applications/misc/ranger/default.nix
@ -7,13 +7,13 @@ assert imagePreviewSupport -> w3m != null;

 python3Packages.buildPythonApplication rec {
  name = "ranger-${version}";
-  version = "1.9.1";
+  version = "1.9.2";

  src = fetchFromGitHub {
    owner = "ranger";
    repo = "ranger";
    rev = "v${version}";
-    sha256= "1zhds37j1scxa9b183qbrjwxqldrdk581c5xiy81vg17sndb1kqj";
+    sha256= "1ws6g8z1m1hfp8bv4msvbaa9f7948p687jmc8h69yib4jkv3qyax";
  };

  checkInputs = with python3Packages; [ pytest ];
@ -51,6 +51,6 @@ python3Packages.buildPythonApplication rec {
    homepage = http://ranger.github.io/;
    license = licenses.gpl3;
    platforms = platforms.unix;
-    maintainers = [ maintainers.magnetophon ];
+    maintainers = [ maintainers.toonn maintainers.magnetophon ];
  };
 }
--- a/pkgs/applications/misc/sequeler/default.nix
+++ b/pkgs/applications/misc/sequeler/default.nix
@ -4,7 +4,7 @@


 let
-  version = "0.6.0";
+  version = "0.6.1";
  sqlGda = libgda.override {
    mysqlSupport = true;
    postgresSupport = true;
@ -17,7 +17,7 @@ in stdenv.mkDerivation rec {
    owner = "Alecaddd";
    repo = "sequeler";
    rev = "v${version}";
-    sha256 = "04x3fg665201g3zy66sicfna4vac4n1pmrahbra90gvfzaia1cai";
+    sha256 = "1gafd8bmwpby7gjzfr7q25rrdmyh1f175fxc1yrcr5nplfyzwfnb";
  };

  nativeBuildInputs = [ meson ninja pkgconfig vala gobjectIntrospection gettext wrapGAppsHook python3 desktop-file-utils ];
--- a/pkgs/applications/misc/solaar/default.nix
+++ b/pkgs/applications/misc/solaar/default.nix
@ -1,5 +1,5 @@
-{fetchFromGitHub, stdenv, gtk3, python34Packages, gobjectIntrospection}:
-python34Packages.buildPythonApplication rec {
+{fetchFromGitHub, stdenv, gtk3, pythonPackages, gobjectIntrospection}:
+pythonPackages.buildPythonApplication rec {
  name = "solaar-unstable-${version}";
  version = "2018-02-02";
  namePrefix = "";
@ -10,7 +10,7 @@ python34Packages.buildPythonApplication rec {
    sha256 = "0zy5vmjzdybnjf0mpp8rny11sc43gmm8172svsm9s51h7x0v83y3";
  };

-  propagatedBuildInputs = [python34Packages.pygobject3 python34Packages.pyudev gobjectIntrospection gtk3];
+  propagatedBuildInputs = [pythonPackages.pygobject3 pythonPackages.pyudev gobjectIntrospection gtk3];
  postInstall = ''
    wrapProgram "$out/bin/solaar" \
      --prefix PYTHONPATH : "$PYTHONPATH" \
--- a/pkgs/applications/networking/browsers/chromium/common.nix
+++ b/pkgs/applications/networking/browsers/chromium/common.nix
@ -1,4 +1,4 @@
-{ stdenv, ninja, which, nodejs, fetchurl, fetchpatch, gnutar
+{ stdenv, gn, ninja, which, nodejs, fetchurl, fetchpatch, gnutar

 # default dependencies
 , bzip2, flac, speex, libopus
@ -139,11 +139,6 @@ let
    # (gentooPatch "<patch>" "0000000000000000000000000000000000000000000000000000000000000000")
      ./patches/fix-freetype.patch
      ./patches/nix_plugin_paths_68.patch
-    ]  ++ optionals (versionRange "68" "69") [
-      ./patches/remove-webp-include-68.patch
-      (githubPatch "4d10424f9e2a06978cdd6cdf5403fcaef18e49fc" "11la1jycmr5b5rw89mzcdwznmd2qh28sghvz9klr1qhmsmw1vzjc")
-      (githubPatch "56cb5f7da1025f6db869e840ed34d3b98b9ab899" "04mp5r1yvdvdx6m12g3lw3z51bzh7m3gr73mhblkn4wxdbvi3dcs")
-    ]  ++ optionals (versionAtLeast version "69") [
      ./patches/remove-webp-include-69.patch
    ] ++ optional enableWideVine ./patches/widevine.patch;

@ -243,15 +238,11 @@ let
    configurePhase = ''
      runHook preConfigure

-      # Build gn
-      python tools/gn/bootstrap/bootstrap.py -v -s --no-clean
-      PATH="$PWD/out/Release:$PATH"
-
      # This is to ensure expansion of $out.
      libExecPath="${libExecPath}"
      python build/linux/unbundle/replace_gn_files.py \
        --system-libraries ${toString gnSystemLibraries}
-      gn gen --args=${escapeShellArg gnFlags} out/Release | tee gn-gen-outputs.txt
+      ${gn}/bin/gn gen --args=${escapeShellArg gnFlags} out/Release | tee gn-gen-outputs.txt

      # Fail if `gn gen` contains a WARNING.
      grep -o WARNING gn-gen-outputs.txt && echo "Found gn WARNING, exiting nix build" && exit 1
--- a/pkgs/applications/networking/browsers/chromium/patches/remove-webp-include-68.patch
+++ b/pkgs/applications/networking/browsers/chromium/patches/remove-webp-include-68.patch
@ -1,12 +0,0 @@
--- a/third_party/blink/renderer/platform/image-encoders/image_encoder.h
-+++ b/third_party/blink/renderer/platform/image-encoders/image_encoder.h
-@@ -8,7 +8,7 @@
- #include "third_party/blink/renderer/platform/platform_export.h"
- #include "third_party/blink/renderer/platform/wtf/vector.h"
- #include "third_party/libjpeg/jpeglib.h"          // for JPEG_MAX_DIMENSION
-#include "third_party/libwebp/src/webp/encode.h"  // for WEBP_MAX_DIMENSION
-+#define WEBP_MAX_DIMENSION 16383
- #include "third_party/skia/include/core/SkStream.h"
- #include "third_party/skia/include/encode/SkJpegEncoder.h"
- #include "third_party/skia/include/encode/SkPngEncoder.h"
-
--- a/pkgs/applications/networking/browsers/chromium/upstream-info.nix
+++ b/pkgs/applications/networking/browsers/chromium/upstream-info.nix
@ -1,18 +1,18 @@
 # This file is autogenerated from update.sh in the same directory.
 {
  beta = {
-    sha256 = "0w5k1446j45796vj8p6kv5cdrkrxyr7rh8d8vavplfldbvg36bdw";
-    sha256bin64 = "0a7gmbcps3b85rhwgrvg41m9db2n3igwr4hncm7kcqnq5hr60v8s";
-    version = "69.0.3497.32";
+    sha256 = "0i3iz6c05ykqxbq58sx954nky0gd0schl7ik2r56p3jqsk8cfnhn";
+    sha256bin64 = "03k5y1nyzx26mxwxmdijkl2kj49vm5vhbxhakfxxjg3r1v0rsqrs";
+    version = "69.0.3497.81";
  };
  dev = {
-    sha256 = "15gk2jbjv3iy4hg4xm1f66x5jqfqh9f98wfzrcsd5ix3ki3f9g3c";
-    sha256bin64 = "1lir6q31dnjsbrz99bfx74r5j6f0c1a443ky1k0idbx6ysvr8nnm";
-    version = "70.0.3521.2";
+    sha256 = "1lx6dfd6w675b4kyrci8ikc8rfmjc1aqmm7bimxp3h4p97j5wml1";
+    sha256bin64 = "0fsxj9h25glp3akw0x2rc488w5zr5v5yvl6ry7fy8w70fqgynffj";
+    version = "70.0.3538.9";
  };
  stable = {
-    sha256 = "1676y2axl5ihvv8jid2i9wp4i4awxzij5nwvd5zx98506l3088bh";
-    sha256bin64 = "0d352maw1630g0hns3c0g0n95bp5iqh7nzs8bnv48kxz87snmpdj";
-    version = "68.0.3440.106";
+    sha256 = "0i3iz6c05ykqxbq58sx954nky0gd0schl7ik2r56p3jqsk8cfnhn";
+    sha256bin64 = "1f3shb85jynxq37vjxxkkxrjayqgvpss1zws5i28x6i9nygfzay7";
+    version = "69.0.3497.81";
  };
 }
--- a/pkgs/applications/networking/browsers/firefox-bin/release_sources.nix
+++ b/pkgs/applications/networking/browsers/firefox-bin/release_sources.nix
--- a/pkgs/applications/networking/browsers/firefox/packages.nix
+++ b/pkgs/applications/networking/browsers/firefox/packages.nix
@ -20,10 +20,10 @@ rec {

  firefox = common rec {
    pname = "firefox";
-    version = "61.0.2";
+    version = "62.0";
    src = fetchurl {
      url = "mirror://mozilla/firefox/releases/${version}/source/firefox-${version}.source.tar.xz";
-      sha512 = "3zzcxqjpsn2m5z4l66rxrq7yf58aii370jj8pcl50smcd55sfsyknnc20agbppsw4k4pnwycfn57im33swwkjzg0hk0h2ng4rvi42x2";
+      sha512 = "0byxslbgr37sm1ra3wywl5c2a39qbkjwc227yp4j2l930m5j86m5g7rmv8zm944vv5vnyzmwhym972si229fm2lwq74p4xam5rfv948";
    };

    patches = nixpkgsPatches ++ [
@ -60,6 +60,7 @@ rec {

    meta = firefox.meta // {
      description = "A web browser built from Firefox Extended Support Release source tree";
+      knownVulnerabilities = [ "Support ended in August 2018." ];
    };
    updateScript = callPackage ./update.nix {
      attrPath = "firefox-esr-52-unwrapped";
@ -69,10 +70,10 @@ rec {

  firefox-esr-60 = common rec {
    pname = "firefox-esr";
-    version = "60.1.0esr";
+    version = "60.2.0esr";
    src = fetchurl {
      url = "mirror://mozilla/firefox/releases/${version}/source/firefox-${version}.source.tar.xz";
-      sha512 = "2bg7zvkpy1x2ryiazvk4nn5m94v0addbhrcrlcf9djnqjf14rp5q50lbiymhxxz0988vgpicsvizifb8gb3hi7b8g17rdw6438ddhh6";
+      sha512 = "1nf7nsycvzafvy4jjli5xh59d2mac17gfx91a1jh86f41w6qcsi3lvkfa8xhxsq8wfdsmqk1f4hmqzyx63h4m691qji7838g2nk49k7";
    };

    patches = nixpkgsPatches ++ [
--- a/pkgs/applications/networking/cluster/helm/default.nix
+++ b/pkgs/applications/networking/cluster/helm/default.nix
@ -5,10 +5,10 @@ let
         then "linux-amd64"
         else "darwin-amd64";
  checksum = if isLinux
-             then "1fk6w6sajdi6iphxrzi9r7xfyaf923nxcqnl01s6x3f611fjvbjn"
-             else "1jzgy641hm3khj0bakfbr5wd5zl3s7w5jb622fjv2jxwmnv7dxiv";
+             then "1zig6ihmxcaw2wsbdd85yf1zswqcifw0hvbp1zws7r5ihd4yv8hg"
+             else "1l8y9i8vhibhwbn5kn5qp722q4dcx464kymlzy2bkmhiqbxnnkkw";
  pname = "helm";
-  version = "2.9.1";
+  version = "2.10.0";
 in
 stdenv.mkDerivation {
  name = "${pname}-${version}";
--- a/pkgs/applications/networking/cluster/kops/default.nix
+++ b/pkgs/applications/networking/cluster/kops/default.nix
@ -3,7 +3,7 @@

 buildGoPackage rec {
  name = "kops-${version}";
-  version = "1.9.0";
+  version = "1.10.0";

  goPackagePath = "k8s.io/kops";

@ -11,7 +11,7 @@ buildGoPackage rec {
    rev = version;
    owner = "kubernetes";
    repo = "kops";
-    sha256 = "03avkm7gk2dqyvd7245qsca1sbhwk41j9yhc208gcmjgjhkx2vn7";
+    sha256 = "1ga83sbhvhcazran6xfwgv95sg8ygg2w59vql0yjicj8r2q01vqp";
  };

  buildInputs = [go-bindata];
--- a/pkgs/applications/networking/instant-messengers/nheko/default.nix
+++ b/pkgs/applications/networking/instant-messengers/nheko/default.nix
@ -1,39 +1,9 @@
-{
-  lib, stdenv, fetchFromGitHub, fetchurl,
-  cmake, doxygen, lmdb, qt5, qtmacextras
+{ lib, stdenv, fetchFromGitHub, fetchurl
+, cmake, lmdb, qt5, qtmacextras, mtxclient
+, boost, spdlog, olm, pkgconfig
 }:

 let
-  json_hpp = fetchurl {
-    url = https://github.com/nlohmann/json/releases/download/v3.1.2/json.hpp;
-    sha256 = "fbdfec4b4cf63b3b565d09f87e6c3c183bdd45c5be1864d3fcb338f6f02c1733";
-  };
-
-  variant_hpp = fetchurl {
-    url = https://github.com/mpark/variant/releases/download/v1.3.0/variant.hpp;
-    sha256 = "1vjiz1x5l8ynqqyb5l9mlrzgps526v45hbmwjilv4brgyi5445fq";
-  };
-
-  matrix-structs = stdenv.mkDerivation rec {
-    name = "matrix-structs-git";
-
-    src = fetchFromGitHub {
-      owner = "mujx";
-      repo = "matrix-structs";
-      rev = "5e57c2385a79b6629d1998fec4a7c0baee23555e";
-      sha256 = "112b7gnvr04g1ak7fnc7ch7w2n825j4qkw0jb49xx06ag93nb6m6";
-    };
-
-    postUnpack = ''
-      cp ${json_hpp} "$sourceRoot/include/json.hpp"
-      cp ${variant_hpp} "$sourceRoot/include/variant.hpp"
-    '';
-
-    patches = [ ./fetchurls.patch ];
-
-    nativeBuildInputs = [ cmake doxygen ];
-  };
-
  tweeny = fetchFromGitHub {
    owner = "mobius3";
    repo = "tweeny";
@ -50,19 +20,15 @@ let
 in
 stdenv.mkDerivation rec {
  name = "nheko-${version}";
-  version = "0.4.3";
+  version = "0.5.5";

  src = fetchFromGitHub {
    owner = "mujx";
    repo = "nheko";
    rev = "v${version}";
-    sha256 = "0qjia42nam3hj835k2jb5b6j6n56rdkb8rn67yqf45xdz8ypmbmv";
+    sha256 = "0k5gmfwmisfavliyz0nfsmwy317ps8a4r3l1d831giqp9pvqvi0i";
  };

-  # This patch is likely not strictly speaking needed, but will help detect when
-  # a dependency is updated, so that the fetches up there can be updated too
-  patches = [ ./external-deps.patch ];
-
  # If, on Darwin, you encounter the error
  #   error: must specify at least one argument for '...' parameter of variadic
  #   macro [-Werror,-Wgnu-zero-variadic-macro-arguments]
@ -79,25 +45,30 @@ stdenv.mkDerivation rec {
  #  export CFLAGS=-Wno-error=gnu-zero-variadic-macro-arguments
  #'';

+  postPatch = ''
+    mkdir -p .deps/include/
+    ln -s ${tweeny}/include .deps/include/tweeny
+    ln -s ${spdlog} .deps/spdlog
+  '';
+
  cmakeFlags = [
-    "-DMATRIX_STRUCTS_LIBRARY=${matrix-structs}/lib/static/libmatrix_structs.a"
-    "-DMATRIX_STRUCTS_INCLUDE_DIR=${matrix-structs}/include/matrix_structs"
-    "-DTWEENY_INCLUDE_DIR=${tweeny}/include"
+    "-DTWEENY_INCLUDE_DIR=.deps/include"
    "-DLMDBXX_INCLUDE_DIR=${lmdbxx}"
  ];

-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake pkgconfig ];

  buildInputs = [
-    lmdb lmdbxx matrix-structs qt5.qtbase qt5.qtmultimedia qt5.qttools tweeny
+    mtxclient olm boost lmdb spdlog
+    qt5.qtbase qt5.qtmultimedia qt5.qttools
  ] ++ lib.optional stdenv.isDarwin qtmacextras;

  enableParallelBuilding = true;

  meta = with stdenv.lib; {
    description = "Desktop client for the Matrix protocol";
-    maintainers = with maintainers; [ ekleog ];
-    platforms = platforms.all;
+    maintainers = with maintainers; [ ekleog fpletz ];
+    platforms = platforms.unix;
    license = licenses.gpl3Plus;
  };
 }
--- a/pkgs/applications/networking/instant-messengers/nheko/external-deps.patch
+++ b/pkgs/applications/networking/instant-messengers/nheko/external-deps.patch
@ -1,94 +0,0 @@
-diff --git a/cmake/LMDBXX.cmake b/cmake/LMDBXX.cmake
-index 3b9817d..e69de29 100644
--- a/cmake/LMDBXX.cmake
-+++ b/cmake/LMDBXX.cmake
-@@ -1,23 +0,0 @@
-include(ExternalProject)
-
-#
-# Build lmdbxx.
-#
-
-set(THIRD_PARTY_ROOT ${CMAKE_SOURCE_DIR}/.third-party)
-set(LMDBXX_ROOT ${THIRD_PARTY_ROOT}/lmdbxx)
-
-set(LMDBXX_INCLUDE_DIR ${LMDBXX_ROOT})
-
-ExternalProject_Add(
-  lmdbxx
-
-  GIT_REPOSITORY https://github.com/bendiken/lmdbxx
-  GIT_TAG 0b43ca87d8cfabba392dfe884eb1edb83874de02
-
-  BUILD_IN_SOURCE 1
-  SOURCE_DIR ${LMDBXX_ROOT}
-  CONFIGURE_COMMAND ""
-  BUILD_COMMAND ""
-  INSTALL_COMMAND ""
-)
-diff --git a/cmake/MatrixStructs.cmake b/cmake/MatrixStructs.cmake
-index cef00f6..e69de29 100644
--- a/cmake/MatrixStructs.cmake
-+++ b/cmake/MatrixStructs.cmake
-@@ -1,33 +0,0 @@
-include(ExternalProject)
-
-#
-# Build matrix-structs.
-#
-
-set(THIRD_PARTY_ROOT ${CMAKE_SOURCE_DIR}/.third-party)
-set(MATRIX_STRUCTS_ROOT ${THIRD_PARTY_ROOT}/matrix_structs)
-set(MATRIX_STRUCTS_INCLUDE_DIR ${MATRIX_STRUCTS_ROOT}/include)
-set(MATRIX_STRUCTS_LIBRARY matrix_structs)
-
-link_directories(${MATRIX_STRUCTS_ROOT})
-
-set(WINDOWS_FLAGS "")
-
-if(MSVC)
-    set(WINDOWS_FLAGS "-DCMAKE_GENERATOR_PLATFORM=x64")
-endif()
-
-ExternalProject_Add(
-  MatrixStructs
-
-  GIT_REPOSITORY https://github.com/mujx/matrix-structs
-  GIT_TAG 5e57c2385a79b6629d1998fec4a7c0baee23555e
-
-  BUILD_IN_SOURCE 1
-  SOURCE_DIR ${MATRIX_STRUCTS_ROOT}
-  CONFIGURE_COMMAND ${CMAKE_COMMAND}
-    -DCMAKE_BUILD_TYPE=Release ${MATRIX_STRUCTS_ROOT}
-    ${WINDOWS_FLAGS}
-  BUILD_COMMAND ${CMAKE_COMMAND} --build ${MATRIX_STRUCTS_ROOT} --config Release
-  INSTALL_COMMAND ""
-)
-diff --git a/cmake/Tweeny.cmake b/cmake/Tweeny.cmake
-index 537ac92..e69de29 100644
--- a/cmake/Tweeny.cmake
-+++ b/cmake/Tweeny.cmake
-@@ -1,23 +0,0 @@
-include(ExternalProject)
-
-#
-# Build tweeny
-#
-
-set(THIRD_PARTY_ROOT ${CMAKE_SOURCE_DIR}/.third-party)
-set(TWEENY_ROOT ${THIRD_PARTY_ROOT}/tweeny)
-
-set(TWEENY_INCLUDE_DIR ${TWEENY_ROOT}/include)
-
-ExternalProject_Add(
-  Tweeny
-
-  GIT_REPOSITORY https://github.com/mobius3/tweeny
-  GIT_TAG b94ce07cfb02a0eb8ac8aaf66137dabdaea857cf
-
-  BUILD_IN_SOURCE 1
-  SOURCE_DIR ${TWEENY_ROOT}
-  CONFIGURE_COMMAND ""
-  BUILD_COMMAND ""
-  INSTALL_COMMAND ""
-)
--- a/pkgs/applications/networking/instant-messengers/nheko/fetchurls.patch
+++ b/pkgs/applications/networking/instant-messengers/nheko/fetchurls.patch
@ -1,21 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 077ac37..c639d71 100644
--- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -18,16 +18,6 @@ include(Doxygen)
- #
- include(CompilerFlags)
- 
-file(DOWNLOAD
-    "https://github.com/nlohmann/json/releases/download/v3.1.2/json.hpp"
-    ${PROJECT_SOURCE_DIR}/include/json.hpp
-    EXPECTED_HASH SHA256=fbdfec4b4cf63b3b565d09f87e6c3c183bdd45c5be1864d3fcb338f6f02c1733)
-
-file(DOWNLOAD
-    "https://github.com/mpark/variant/releases/download/v1.3.0/variant.hpp"
-    ${PROJECT_SOURCE_DIR}/include/variant.hpp
-    EXPECTED_MD5 "be0ce322cdd408e1b347b9f1d59ea67a")
-
- include_directories(include)
- 
- set(SRC
--- a/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix
+++ b/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix
@ -55,11 +55,11 @@ let

 in stdenv.mkDerivation rec {
  name = "signal-desktop-${version}";
-  version = "1.15.5";
+  version = "1.16.0";

  src = fetchurl {
    url = "https://updates.signal.org/desktop/apt/pool/main/s/signal-desktop/signal-desktop_${version}_amd64.deb";
-    sha256 = "1a63kyxbhdaz6izprg8wryvscmvfjii50xi1v5pxlf74x2pkxs8k";
+    sha256 = "0hw5h1m8fijhqybx0xijrkifn5wl50qibaxkn2mxqf4mjwlvaw9a";
  };

  phases = [ "unpackPhase" "installPhase" ];
--- a/pkgs/applications/networking/irc/weechat/aggregate-commands.patch
+++ b/pkgs/applications/networking/irc/weechat/aggregate-commands.patch
@ -0,0 +1,110 @@
+diff --git a/src/core/wee-command.c b/src/core/wee-command.c
+index 91c3c068d..8105e4171 100644
+--- a/src/core/wee-command.c
+++ b/src/core/wee-command.c
+@@ -8345,10 +8345,20 @@ command_exec_list (const char *command_list)
+ void
+ command_startup (int plugins_loaded)
+ {
+    int i;
+
+     if (plugins_loaded)
+     {
+         command_exec_list (CONFIG_STRING(config_startup_command_after_plugins));
+-        command_exec_list (weechat_startup_commands);
+        if (weechat_startup_commands)
+        {
+            for (i = 0; i < weelist_size (weechat_startup_commands); i++)
+            {
+                command_exec_list (
+                    weelist_string (
+                        weelist_get (weechat_startup_commands, i)));
+            }
+        }
+     }
+     else
+         command_exec_list (CONFIG_STRING(config_startup_command_before_plugins));
+diff --git a/src/core/weechat.c b/src/core/weechat.c
+index f74598ad5..ff2e539d1 100644
+--- a/src/core/weechat.c
+++ b/src/core/weechat.c
+@@ -60,6 +60,7 @@
+ #include "wee-eval.h"
+ #include "wee-hdata.h"
+ #include "wee-hook.h"
+#include "wee-list.h"
+ #include "wee-log.h"
+ #include "wee-network.h"
+ #include "wee-proxy.h"
+@@ -102,7 +103,8 @@ int weechat_no_gnutls = 0;             /* remove init/deinit of gnutls      */
+                                        /* (useful with valgrind/electric-f.)*/
+ int weechat_no_gcrypt = 0;             /* remove init/deinit of gcrypt      */
+                                        /* (useful with valgrind)            */
+-char *weechat_startup_commands = NULL; /* startup commands (-r flag)        */
+struct t_weelist *weechat_startup_commands = NULL; /* startup commands      */
+                                                   /* (option -r)           */
+ 
+ 
+ /*
+@@ -152,9 +154,13 @@ weechat_display_usage ()
+           "  -h, --help               display this help\n"
+           "  -l, --license            display WeeChat license\n"
+           "  -p, --no-plugin          don't load any plugin at startup\n"
+-          "  -r, --run-command <cmd>  run command(s) after startup\n"
+-          "                           (many commands can be separated by "
+-          "semicolons)\n"
+          "  -P, --plugins <plugins>  load only these plugins at startup\n"
+          "                           (see /help weechat.plugin.autoload)\n"
+          "  -r, --run-command <cmd>  run command(s) after startup;\n"
+          "                           many commands can be separated by "
+          "semicolons,\n"
+          "                           this option can be given multiple "
+          "times\n"
+           "  -s, --no-script          don't load any script at startup\n"
+           "      --upgrade            upgrade WeeChat using session files "
+           "(see /help upgrade in WeeChat)\n"
+@@ -276,9 +282,10 @@ weechat_parse_args (int argc, char *argv[])
+         {
+             if (i + 1 < argc)
+             {
+-                if (weechat_startup_commands)
+-                    free (weechat_startup_commands);
+-                weechat_startup_commands = strdup (argv[++i]);
+                if (!weechat_startup_commands)
+                    weechat_startup_commands = weelist_new ();
+                weelist_add (weechat_startup_commands, argv[++i],
+                             WEECHAT_LIST_POS_END, NULL);
+             }
+             else
+             {
+@@ -616,6 +623,8 @@ weechat_shutdown (int return_code, int crash)
+         free (weechat_home);
+     if (weechat_local_charset)
+         free (weechat_local_charset);
+    if (weechat_startup_commands)
+        weelist_free (weechat_startup_commands);
+ 
+     if (crash)
+         abort ();
+diff --git a/src/core/weechat.h b/src/core/weechat.h
+index 9420ff415..cbb565a03 100644
+--- a/src/core/weechat.h
+++ b/src/core/weechat.h
+@@ -96,6 +96,8 @@
+ /* name of environment variable with an extra lib dir */
+ #define WEECHAT_EXTRA_LIBDIR "WEECHAT_EXTRA_LIBDIR"
+ 
+struct t_weelist;
+
+ /* global variables and functions */
+ extern int weechat_headless;
+ extern int weechat_debug_core;
+@@ -112,7 +114,7 @@ extern char *weechat_local_charset;
+ extern int weechat_plugin_no_dlclose;
+ extern int weechat_no_gnutls;
+ extern int weechat_no_gcrypt;
+-extern char *weechat_startup_commands;
+extern struct t_weelist *weechat_startup_commands;
+ 
+ extern void weechat_term_check ();
+ extern void weechat_shutdown (int return_code, int crash);
--- a/pkgs/applications/networking/irc/weechat/default.nix
+++ b/pkgs/applications/networking/irc/weechat/default.nix
@ -12,7 +12,8 @@
 , tclSupport ? true, tcl
 , extraBuildInputs ? []
 , configure ? { availablePlugins, ... }: { plugins = builtins.attrValues availablePlugins; }
-, runCommand }:
+, runCommand, buildEnv
+}:

 let
  inherit (pythonPackages) python;
@ -29,12 +30,12 @@ let
  weechat =
    assert lib.all (p: p.enabled -> ! (builtins.elem null p.buildInputs)) plugins;
    stdenv.mkDerivation rec {
-      version = "2.1";
+      version = "2.2";
      name = "weechat-${version}";

      src = fetchurl {
        url = "http://weechat.org/files/src/weechat-${version}.tar.bz2";
-        sha256 = "0fq68wgynv2c3319gmzi0lz4ln4yrrk755y5mbrlr7fc1sx7ffd8";
+        sha256 = "0p4nhh7f7w4q77g7jm9i6fynndqlgjkc9dk5g1xb4gf9imiisqlg";
      };

      outputs = [ "out" "man" ] ++ map (p: p.name) enabledPlugins;
@ -69,6 +70,13 @@ let
        done
      '';

+      # remove when bumping to the latest version.
+      # This patch basically rebases `fcf7469d7664f37e94d5f6d0b3fe6fce6413f88c`
+      # from weechat upstream to weechat-2.2.
+      patches = [
+        ./aggregate-commands.patch
+      ];
+
      meta = {
        homepage = http://www.weechat.org/;
        description = "A fast, light and extensible chat client";
@ -78,38 +86,38 @@ let
          on https://nixos.org/nixpkgs/manual/#sec-weechat .
        '';
        license = stdenv.lib.licenses.gpl3;
-        maintainers = with stdenv.lib.maintainers; [ lovek323 garbas the-kenny lheckemann ];
+        maintainers = with stdenv.lib.maintainers; [ lovek323 garbas the-kenny lheckemann ma27 ];
        platforms = stdenv.lib.platforms.unix;
      };
    };
 in if configure == null then weechat else
  let
    perlInterpreter = perl;
-    config = configure {
-      availablePlugins = let
-          simplePlugin = name: {pluginFile = "${weechat.${name}}/lib/weechat/plugins/${name}.so";};
-        in rec {
-          python = {
-            pluginFile = "${weechat.python}/lib/weechat/plugins/python.so";
-            withPackages = pkgsFun: (python // {
-              extraEnv = ''
-                export PYTHONHOME="${pythonPackages.python.withPackages pkgsFun}"
-              '';
-            });
-          };
-          perl = (simplePlugin "perl") // {
+    availablePlugins = let
+        simplePlugin = name: {pluginFile = "${weechat.${name}}/lib/weechat/plugins/${name}.so";};
+      in rec {
+        python = {
+          pluginFile = "${weechat.python}/lib/weechat/plugins/python.so";
+          withPackages = pkgsFun: (python // {
            extraEnv = ''
-              export PATH="${perlInterpreter}/bin:$PATH"
+              export PYTHONHOME="${pythonPackages.python.withPackages pkgsFun}"
            '';
-          };
-          tcl = simplePlugin "tcl";
-          ruby = simplePlugin "ruby";
-          guile = simplePlugin "guile";
-          lua = simplePlugin "lua";
+          });
        };
+        perl = (simplePlugin "perl") // {
+          extraEnv = ''
+            export PATH="${perlInterpreter}/bin:$PATH"
+          '';
+        };
+        tcl = simplePlugin "tcl";
+        ruby = simplePlugin "ruby";
+        guile = simplePlugin "guile";
+        lua = simplePlugin "lua";
      };

-    inherit (config) plugins;
+    config = configure { inherit availablePlugins; };
+
+    plugins = config.plugins or (builtins.attrValues availablePlugins);

    pluginsDir = runCommand "weechat-plugins" {} ''
      mkdir -p $out/plugins
@ -117,13 +125,29 @@ in if configure == null then weechat else
        ln -s $plugin $out/plugins
      done
    '';
-  in (writeScriptBin "weechat" ''
-    #!${stdenv.shell}
-    export WEECHAT_EXTRA_LIBDIR=${pluginsDir}
-    ${lib.concatMapStringsSep "\n" (p: lib.optionalString (p ? extraEnv) p.extraEnv) plugins}
-    exec ${weechat}/bin/weechat "$@"
-  '') // {
-    name = weechat.name;
-    unwrapped = weechat;
-    meta = weechat.meta;
+
+    init = let
+      init = builtins.replaceStrings [ "\n" ] [ ";" ] (config.init or "");
+
+      mkScript = drv: lib.flip map drv.scripts (script: "/script load ${drv}/share/${script}");
+
+      scripts = builtins.concatStringsSep ";" (lib.foldl (scripts: drv: scripts ++ mkScript drv)
+        [ ] (config.scripts or []));
+    in "${scripts};${init}";
+
+    mkWeechat = bin: (writeScriptBin bin ''
+      #!${stdenv.shell}
+      export WEECHAT_EXTRA_LIBDIR=${pluginsDir}
+      ${lib.concatMapStringsSep "\n" (p: lib.optionalString (p ? extraEnv) p.extraEnv) plugins}
+      exec ${weechat}/bin/${bin} "$@" --run-command ${lib.escapeShellArg init}
+    '') // {
+      inherit (weechat) name meta;
+      unwrapped = weechat;
+    };
+  in buildEnv {
+    name = "weechat-bin-env";
+    paths = [
+      (mkWeechat "weechat")
+      (mkWeechat "weechat-headless")
+    ];
  }
--- a/pkgs/applications/networking/irc/weechat/scripts/default.nix
+++ b/pkgs/applications/networking/irc/weechat/scripts/default.nix
@ -0,0 +1,13 @@
+{ callPackage, luaPackages, pythonPackages }:
+
+{
+  weechat-xmpp = callPackage ./weechat-xmpp {
+    inherit (pythonPackages) pydns;
+  };
+
+  weechat-matrix-bridge = callPackage ./weechat-matrix-bridge {
+    inherit (luaPackages) cjson;
+  };
+
+  wee-slack = callPackage ./wee-slack { };
+}
--- a/pkgs/applications/networking/irc/weechat/scripts/wee-slack/default.nix
+++ b/pkgs/applications/networking/irc/weechat/scripts/wee-slack/default.nix
@ -0,0 +1,29 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  name = "wee-slack-${version}";
+  version = "2.1.1";
+
+  src = fetchFromGitHub {
+    repo = "wee-slack";
+    owner = "wee-slack";
+    rev = "v${version}";
+    sha256 = "05caackz645aw6kljmiihiy7xz9jld8b9blwpmh0cnaihavgj1wc";
+  };
+
+  passthru.scripts = [ "wee_slack.py" ];
+
+  installPhase = ''
+    mkdir -p $out/share
+    cp wee_slack.py $out/share/wee_slack.py
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/wee-slack/wee-slack;
+    license = licenses.mit;
+    maintainers = with maintainers; [ ma27 ];
+    description = ''
+      A WeeChat plugin for Slack.com. Synchronizes read markers, provides typing notification, search, etc..
+    '';
+  };
+}
--- a/pkgs/applications/networking/irc/weechat/scripts/weechat-matrix-bridge/default.nix
+++ b/pkgs/applications/networking/irc/weechat/scripts/weechat-matrix-bridge/default.nix
@ -25,6 +25,8 @@ stdenv.mkDerivation {
      --replace "__NIX_LIB_PATH__" "$out/lib/?.so"
  '';

+  passthru.scripts = [ "olm.lua" "matrix.lua" ];
+
  installPhase = ''
    mkdir -p $out/{share,lib}

--- a/pkgs/applications/networking/irc/weechat/scripts/weechat-matrix-bridge/library-path.patch
+++ b/pkgs/applications/networking/irc/weechat/scripts/weechat-matrix-bridge/library-path.patch
--- a/pkgs/applications/networking/irc/weechat/scripts/weechat-xmpp/default.nix
+++ b/pkgs/applications/networking/irc/weechat/scripts/weechat-xmpp/default.nix
@ -25,6 +25,8 @@ stdenv.mkDerivation {
    })
  ];

+  passthru.scripts = [ "jabber.py" ];
+
  meta = with stdenv.lib; {
    description = "A fork of the jabber plugin for weechat";
    homepage = "https://github.com/sleduc/weechat-xmpp";
--- a/pkgs/applications/networking/irc/weechat/scripts/weechat-xmpp/libpath.patch
+++ b/pkgs/applications/networking/irc/weechat/scripts/weechat-xmpp/libpath.patch
--- a/pkgs/applications/networking/p2p/opentracker/default.nix
+++ b/pkgs/applications/networking/p2p/opentracker/default.nix
@ -1,20 +1,20 @@
 { stdenv, fetchgit, libowfat, zlib }:

 stdenv.mkDerivation {
-  name = "opentracker-2016-10-02";
+  name = "opentracker-2018-05-26";

  src = fetchgit {
-    url = "git://erdgeist.org/opentracker";
-    rev = "0ebc0ed6a3e3b7acc9f9e338cc23cea5f4f22f61";
-    sha256 = "0qi0a8fygjwgs3yacramfn53jdabfgrlzid7q597x9lr94anfpyl";
+    url = "https://erdgeist.org/gitweb/opentracker";
+    rev = "6411f1567f64248b0d145493c2e61004d2822623";
+    sha256 = "110nfb6n4clykwdzpk54iccsfjawq0krjfqhg114i1z0ri5dyl8j";
  };

  buildInputs = [ libowfat zlib ];

  installPhase = ''
-    mkdir -p $out/bin $out/share/doc
-    cp opentracker $out/bin
-    cp opentracker.conf.sample $out/share/doc
+    runHook preInstall
+    install -D opentracker $out/bin/opentracker
+    install -D opentracker.conf.sample $out/share/doc/opentracker.conf.sample
    runHook postInstall
  '';

--- a/pkgs/applications/networking/sync/rclone/default.nix
+++ b/pkgs/applications/networking/sync/rclone/default.nix
@ -2,7 +2,7 @@

 buildGoPackage rec {
  name = "rclone-${version}";
-  version = "1.43";
+  version = "1.43.1";

  goPackagePath = "github.com/ncw/rclone";

@ -10,7 +10,7 @@ buildGoPackage rec {
    owner = "ncw";
    repo = "rclone";
    rev = "v${version}";
-    sha256 = "1khg5jsrjmnblv8zg0zqs1n0hmjv05pjj94m9d7jbp9d936lxsxx";
+    sha256 = "0iz427gdm8cxx3kbjmhw7jsvi9j0ppb5aqcq4alwf72fvpvql3mx";
  };

  outputs = [ "bin" "out" "man" ];
--- a/pkgs/applications/networking/testssl/default.nix
+++ b/pkgs/applications/networking/testssl/default.nix
@ -2,7 +2,7 @@
 , dnsutils, coreutils, openssl, nettools, utillinux, procps }:

 let
-  version = "2.9.5-5";
+  version = "2.9.5-6";

 in stdenv.mkDerivation rec {
  name = "testssl.sh-${version}";
@ -11,7 +11,7 @@ in stdenv.mkDerivation rec {
    owner = "drwetter";
    repo = "testssl.sh";
    rev = "v${version}";
-    sha256 = "0zgj9vhd8fv3a1cn8dxqmjd8qmgryc867gq7zbvbr41lkqc06a1r";
+    sha256 = "0wn7lxz0ibv59v0acbsk5z3rsmr65zr1q7n4kxva1cw5xzq9ya6k";
  };

  nativeBuildInputs = [ makeWrapper ];
--- a/pkgs/applications/science/astronomy/gildas/default.nix
+++ b/pkgs/applications/science/astronomy/gildas/default.nix
@ -12,7 +12,10 @@ stdenv.mkDerivation rec {
  name = "gildas-${version}";

  src = fetchurl {
-    url = "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.gz";
+    # For each new release, the upstream developers of Gildas move the
+    # source code of the previous release to a different directory
+    urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.gz"
+      "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.gz" ];
    sha256 = "0mg3wijrj8x1p912vkgrhxbypjx7aj9b1492yxvq2y3fxban6bj1";
  };

--- a/pkgs/applications/science/biology/hisat2/default.nix
+++ b/pkgs/applications/science/biology/hisat2/default.nix
@ -0,0 +1,49 @@
+{stdenv, fetchurl, unzip, which, python}:
+
+stdenv.mkDerivation rec {
+  name = "hisat2-${version}";
+  version = "2.1.0";
+
+  src = fetchurl {
+    url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-${version}-source.zip";
+    sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
+  };
+
+  buildInputs = [ unzip  which python ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp hisat2 \
+       hisat2-inspect-l \
+       hisat2-build-s \
+       hisat2-align-l \
+       hisat2-inspect \
+       hisat2-align-s \
+       hisat2-inspect-s \
+       hisat2-build-l \
+       hisat2-build \
+       extract_exons.py \
+       extract_splice_sites.py \
+       hisat2_extract_exons.py \
+       hisat2_extract_snps_haplotypes_UCSC.py \
+       hisat2_extract_snps_haplotypes_VCF.py \
+       hisat2_extract_splice_sites.py \
+       hisat2_simulate_reads.py \
+       hisatgenotype_build_genome.py \
+       hisatgenotype_extract_reads.py \
+       hisatgenotype_extract_vars.py \
+       hisatgenotype_hla_cyp.py \
+       hisatgenotype_locus.py \
+       hisatgenotype.py \
+       $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Graph based aligner";
+    license = licenses.gpl3;
+    homepage = https://ccb.jhu.edu/software/hisat2/index.shtml;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = [ "x86_64-linux" "i686-linux" ];
+  };
+
+}
--- a/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/pkgs/applications/science/biology/picard-tools/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  name = "picard-tools-${version}";
-  version = "2.18.11";
+  version = "2.18.12";

  src = fetchurl {
    url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "03wkyz3bjx3n8bwambhz9lr09271r1wxycmx4p7m2naqs4afxb89";
+    sha256 = "0r5w71fcji4j3xjdhip9jlvmqi66x52af8b7mfxp4nz6xxl9ilxm";
  };

  buildInputs = [ jre makeWrapper ];
--- a/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/pkgs/applications/science/chemistry/jmol/default.nix
@ -17,7 +17,7 @@ let
  };
 in
 stdenv.mkDerivation rec {
-  version = "14.29.17";
+  version = "14.29.19";
  pname = "jmol";
  name = "${pname}-${version}";

@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
    baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
  in fetchurl {
    url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    sha256 = "1dnxbvi8ha9z2ldymkjpxydd216afv6k7fdp3j70sql10zgy0isk";
+    sha256 = "0sfbbi6mgj9hqzvcz19cr5s96rna2f2b1nc1d4j28xvva7qaqjm5";
  };

  patchPhase = ''
--- a/pkgs/applications/science/geometry/drgeo/default.nix
+++ b/pkgs/applications/science/geometry/drgeo/default.nix
@ -20,8 +20,10 @@ stdenv.mkDerivation rec {
    cp drgeo.desktop.in drgeo.desktop
  '';

-  meta = {
+  meta = with stdenv.lib; {
    description = "Interactive geometry program";
-    platforms = stdenv.lib.platforms.linux;
+    homepage = https://sourceforge.net/projects/ofset;
+    license = licenses.gpl2;
+    platforms = platforms.linux;
  };
 }
--- a/pkgs/applications/science/logic/prooftree/default.nix
+++ b/pkgs/applications/science/logic/prooftree/default.nix
@ -15,7 +15,7 @@ stdenv.mkDerivation (rec {
  dontAddPrefix = true;
  configureFlags = [ "--prefix" "$(out)" ];

-  meta = {
+  meta = with stdenv.lib; {
    description = "A program for proof-tree visualization";
    longDescription = ''
      Prooftree is a program for proof-tree visualization during interactive
@ -35,7 +35,8 @@ stdenv.mkDerivation (rec {
      shift-click).
    '';
    homepage = http://askra.de/software/prooftree;
-    platforms = stdenv.lib.platforms.unix;
-    maintainers = [ stdenv.lib.maintainers.jwiegley ];
+    platforms = platforms.unix;
+    maintainers = [ maintainers.jwiegley ];
+    license = licenses.gpl3;
  };
 })
--- a/pkgs/applications/science/math/almonds/default.nix
+++ b/pkgs/applications/science/math/almonds/default.nix
@ -20,8 +20,7 @@ with python3.pkgs; buildPythonApplication rec {
  meta = with stdenv.lib; {
    description = "Terminal Mandelbrot fractal viewer";
    homepage = https://github.com/Tenchi2xh/Almonds;
-    # No license has been specified
-    license = licenses.unfree;
+    license = licenses.mit;
    maintainers = with maintainers; [ infinisil ];
  };
 }
--- a/pkgs/applications/science/math/pynac/default.nix
+++ b/pkgs/applications/science/math/pynac/default.nix
@ -41,6 +41,7 @@ stdenv.mkDerivation rec {
      of the full GiNaC, and it is *only* meant to be used as a Python library.
    '';
    homepage    = http://pynac.org;
+    license = licenses.gpl3;
    maintainers = with maintainers; [ timokau ];
    platforms   = platforms.linux;
  };
--- a/pkgs/applications/science/math/ripser/default.nix
+++ b/pkgs/applications/science/math/ripser/default.nix
@ -8,7 +8,8 @@

 with stdenv.lib;

-assert elem fileFormat ["lowerTriangularCsv" "upperTriangularCsv" "dipha"];
+assert assertOneOf "fileFormat" fileFormat
+  ["lowerTriangularCsv" "upperTriangularCsv" "dipha"];
 assert useGoogleHashmap -> sparsehash != null;

 let
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@ -21,7 +21,7 @@ let

      sagelib = self.callPackage ./sagelib.nix {
        inherit flint ecl arb;
-        inherit sage-src pynac singular;
+        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
        linbox = nixpkgs.linbox.override { withSage = true; };
      };

@ -41,13 +41,13 @@ let
      };

      sage-env = self.callPackage ./sage-env.nix {
-        inherit sage-src python rWrapper ecl singular palp flint pynac pythonEnv;
+        inherit sage-src python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv;
        pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
      };

      sage-with-env = self.callPackage ./sage-with-env.nix {
        inherit pythonEnv;
-        inherit sage-src pynac singular;
+        inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
        pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
        three = nodePackages_8_x.three;
      };
@ -60,6 +60,10 @@ let
    };
  };

+  openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; };
+  openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; };
+  openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; };
+
  sage-src = callPackage ./sage-src.nix {};

  pythonRuntimeDeps = with python.pkgs; [
--- a/pkgs/applications/science/math/sage/openblas-pc.nix
+++ b/pkgs/applications/science/math/sage/openblas-pc.nix
@ -0,0 +1,17 @@
+{ openblasCompat
+, writeTextFile
+, name
+}:
+
+writeTextFile {
+  name = "openblas-${name}-pc-${openblasCompat.version}";
+  destination = "/lib/pkgconfig/${name}.pc";
+  text = ''
+    Name: ${name}
+    Version: ${openblasCompat.version}
+
+    Description: ${name} for SageMath, provided by the OpenBLAS package.
+    Cflags: -I${openblasCompat}/include
+    Libs: -L${openblasCompat}/lib -lopenblas
+  '';
+}
--- a/pkgs/applications/science/math/sage/patches/numpy-1.15.1.patch
+++ b/pkgs/applications/science/math/sage/patches/numpy-1.15.1.patch
@ -1,5 +1,5 @@
 diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst
-index 79b4205fd3..9a89bd2136 100644
+index 2347a1190d..f5b0fe71a4 100644
 --- a/src/doc/en/faq/faq-usage.rst
 +++ b/src/doc/en/faq/faq-usage.rst
@@ -338,7 +338,7 @@ ints. For example::
@ -174,7 +174,7 @@ index 5b89cd75ee..e50b2ea5d4 100644
 This creates a random 5x5 matrix ``A``, and solves `Ax=b` where
 ``b=[0.0,1.0,2.0,3.0,4.0]``. There are many other routines in the :mod:`numpy.linalg`
 diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx
-index df85cce43d..34ea164be0 100644
+index 60f37f7557..4ac3dedf1d 100644
 --- a/src/sage/calculus/riemann.pyx
 +++ b/src/sage/calculus/riemann.pyx
@@ -1191,30 +1191,30 @@ cpdef complex_to_spiderweb(np.ndarray[COMPLEX_T, ndim = 2] z_values,
@ -248,7 +248,7 @@ index df85cce43d..34ea164be0 100644
 
     TESTS::
 diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py
-index 61b1003002..4baee9cbbd 100644
+index 0a9bd61267..d2193cc2d6 100644
 --- a/src/sage/combinat/fully_packed_loop.py
 +++ b/src/sage/combinat/fully_packed_loop.py
@@ -72,11 +72,11 @@ def _make_color_list(n, colors=None,  color_map=None, randomize=False):
@ -269,10 +269,10 @@ index 61b1003002..4baee9cbbd 100644
         ['blue', 'blue', 'red', 'blue', 'red', 'red', 'red', 'blue']
     """
 diff --git a/src/sage/finance/time_series.pyx b/src/sage/finance/time_series.pyx
-index c37700d14e..49b7298d0b 100644
+index 28779365df..3ab0282861 100644
 --- a/src/sage/finance/time_series.pyx
 +++ b/src/sage/finance/time_series.pyx
-@@ -109,8 +109,8 @@ cdef class TimeSeries:
+@@ -111,8 +111,8 @@ cdef class TimeSeries:
 
             sage: import numpy
             sage: v = numpy.array([[1,2], [3,4]], dtype=float); v
@ -283,7 +283,7 @@ index c37700d14e..49b7298d0b 100644
             sage: finance.TimeSeries(v)
             [1.0000, 2.0000, 3.0000, 4.0000]
             sage: finance.TimeSeries(v[:,0])
-@@ -2098,14 +2098,14 @@ cdef class TimeSeries:
+@@ -2100,14 +2100,14 @@ cdef class TimeSeries:
 
             sage: w[0] = 20
             sage: w
@ -301,7 +301,7 @@ index c37700d14e..49b7298d0b 100644
             sage: v
             [20.0000, -3.0000, 4.5000, -2.0000]
 diff --git a/src/sage/functions/hyperbolic.py b/src/sage/functions/hyperbolic.py
-index 931a4b41e4..bf33fc483d 100644
+index aff552f450..7a6df931e7 100644
 --- a/src/sage/functions/hyperbolic.py
 +++ b/src/sage/functions/hyperbolic.py
@@ -214,7 +214,7 @@ class Function_coth(GinacFunction):
@ -341,7 +341,7 @@ index 931a4b41e4..bf33fc483d 100644
         return arctanh(1.0 / x)
 
 diff --git a/src/sage/functions/orthogonal_polys.py b/src/sage/functions/orthogonal_polys.py
-index 017c85a96f..33fbb499c5 100644
+index ed6365bef4..99b8b04dad 100644
 --- a/src/sage/functions/orthogonal_polys.py
 +++ b/src/sage/functions/orthogonal_polys.py
@@ -810,12 +810,12 @@ class Func_chebyshev_T(ChebyshevFunction):
@ -379,10 +379,10 @@ index 017c85a96f..33fbb499c5 100644
             array([ 0.2 , -0.96])
         """
 diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py
-index 679384c907..d63b295a4c 100644
+index 1883daa3e6..9885222817 100644
 --- a/src/sage/functions/other.py
 +++ b/src/sage/functions/other.py
-@@ -390,7 +390,7 @@ class Function_ceil(BuiltinFunction):
+@@ -389,7 +389,7 @@ class Function_ceil(BuiltinFunction):
             sage: import numpy
             sage: a = numpy.linspace(0,2,6)
             sage: ceil(a)
@ -391,7 +391,7 @@ index 679384c907..d63b295a4c 100644
 
         Test pickling::
 
-@@ -539,7 +539,7 @@ class Function_floor(BuiltinFunction):
+@@ -553,7 +553,7 @@ class Function_floor(BuiltinFunction):
             sage: import numpy
             sage: a = numpy.linspace(0,2,6)
             sage: floor(a)
@ -400,7 +400,7 @@ index 679384c907..d63b295a4c 100644
             sage: floor(x)._sympy_()
             floor(x)
 
-@@ -840,7 +840,7 @@ def sqrt(x, *args, **kwds):
+@@ -869,7 +869,7 @@ def sqrt(x, *args, **kwds):
             sage: import numpy
             sage: a = numpy.arange(2,5)
             sage: sqrt(a)
@ -409,11 +409,35 @@ index 679384c907..d63b295a4c 100644
         """
         if isinstance(x, float):
             return math.sqrt(x)
+diff --git a/src/sage/functions/spike_function.py b/src/sage/functions/spike_function.py
+index 1e021de3fe..56635ca98f 100644
+--- a/src/sage/functions/spike_function.py
+++ b/src/sage/functions/spike_function.py
+@@ -157,7 +157,7 @@ class SpikeFunction:
+             sage: S = spike_function([(-3,4),(-1,1),(2,3)]); S
+             A spike function with spikes at [-3.0, -1.0, 2.0]
+             sage: P = S.plot_fft_abs(8)
+-            sage: p = P[0]; p.ydata
+            sage: p = P[0]; p.ydata  # abs tol 1e-8
+             [5.0, 5.0, 3.367958691924177, 3.367958691924177, 4.123105625617661, 4.123105625617661, 4.759921664218055, 4.759921664218055]
+         """
+         w = self.vector(samples = samples, xmin=xmin, xmax=xmax)
+@@ -176,8 +176,8 @@ class SpikeFunction:
+             sage: S = spike_function([(-3,4),(-1,1),(2,3)]); S
+             A spike function with spikes at [-3.0, -1.0, 2.0]
+             sage: P = S.plot_fft_arg(8)
+-            sage: p = P[0]; p.ydata
+-            [0.0, 0.0, -0.211524990023434..., -0.211524990023434..., 0.244978663126864..., 0.244978663126864..., -0.149106180027477..., -0.149106180027477...]
+            sage: p = P[0]; p.ydata  # abs tol 1e-8
+            [0.0, 0.0, -0.211524990023434, -0.211524990023434, 0.244978663126864, 0.244978663126864, -0.149106180027477, -0.149106180027477]
+         """
+         w = self.vector(samples = samples, xmin=xmin, xmax=xmax)
+         xmin, xmax = self._ranges(xmin, xmax)
 diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py
-index e7e7a311cd..e7ff78a9de 100644
+index 501e7ff6b6..5f760912f0 100644
 --- a/src/sage/functions/trig.py
 +++ b/src/sage/functions/trig.py
-@@ -731,7 +731,7 @@ class Function_arccot(GinacFunction):
+@@ -724,7 +724,7 @@ class Function_arccot(GinacFunction):
             sage: import numpy
             sage: a = numpy.arange(2, 5)
             sage: arccot(a)
@ -422,7 +446,7 @@ index e7e7a311cd..e7ff78a9de 100644
         """
         return math.pi/2 - arctan(x)
 
-@@ -787,7 +787,7 @@ class Function_arccsc(GinacFunction):
+@@ -780,7 +780,7 @@ class Function_arccsc(GinacFunction):
             sage: import numpy
             sage: a = numpy.arange(2, 5)
             sage: arccsc(a)
@ -431,7 +455,7 @@ index e7e7a311cd..e7ff78a9de 100644
         """
         return arcsin(1.0/x)
 
-@@ -845,7 +845,7 @@ class Function_arcsec(GinacFunction):
+@@ -838,7 +838,7 @@ class Function_arcsec(GinacFunction):
             sage: import numpy
             sage: a = numpy.arange(2, 5)
             sage: arcsec(a)
@ -440,7 +464,7 @@ index e7e7a311cd..e7ff78a9de 100644
         """
         return arccos(1.0/x)
 
-@@ -920,13 +920,13 @@ class Function_arctan2(GinacFunction):
+@@ -913,13 +913,13 @@ class Function_arctan2(GinacFunction):
             sage: a = numpy.linspace(1, 3, 3)
             sage: b = numpy.linspace(3, 6, 3)
             sage: atan2(a, b)
@ -458,10 +482,10 @@ index e7e7a311cd..e7ff78a9de 100644
         TESTS::
 
 diff --git a/src/sage/matrix/constructor.pyx b/src/sage/matrix/constructor.pyx
-index 19a1d37df0..5780dfae1c 100644
+index 12136f1773..491bf22e62 100644
 --- a/src/sage/matrix/constructor.pyx
 +++ b/src/sage/matrix/constructor.pyx
-@@ -494,8 +494,8 @@ class MatrixFactory(object):
+@@ -503,8 +503,8 @@ def matrix(*args, **kwds):
         [7 8 9]
         Full MatrixSpace of 3 by 3 dense matrices over Integer Ring
         sage: n = matrix(QQ, 2, 2, [1, 1/2, 1/3, 1/4]).numpy(); n
@ -473,10 +497,31 @@ index 19a1d37df0..5780dfae1c 100644
         [  1 1/2]
         [1/3 1/4]
 diff --git a/src/sage/matrix/matrix_double_dense.pyx b/src/sage/matrix/matrix_double_dense.pyx
-index 48e0a8a97f..1be5d35b19 100644
+index 66e54a79a4..0498334f4b 100644
 --- a/src/sage/matrix/matrix_double_dense.pyx
 +++ b/src/sage/matrix/matrix_double_dense.pyx
-@@ -2546,7 +2546,7 @@ cdef class Matrix_double_dense(Matrix_dense):
+@@ -606,6 +606,9 @@ cdef class Matrix_double_dense(Matrix_dense):
+             [ 3.0 + 9.0*I 4.0 + 16.0*I 5.0 + 25.0*I]
+             [6.0 + 36.0*I 7.0 + 49.0*I 8.0 + 64.0*I]
+             sage: B.condition()
+            doctest:warning
+            ...
+            ComplexWarning: Casting complex values to real discards the imaginary part
+             203.851798...
+             sage: B.condition(p='frob')
+             203.851798...
+@@ -654,9 +657,7 @@ cdef class Matrix_double_dense(Matrix_dense):
+             True
+             sage: B = A.change_ring(CDF)
+             sage: B.condition()
+-            Traceback (most recent call last):
+-            ...
+-            LinAlgError: Singular matrix
+            +Infinity
+ 
+         Improper values of ``p`` are caught.  ::
+ 
+@@ -2519,7 +2520,7 @@ cdef class Matrix_double_dense(Matrix_dense):
             sage: P.is_unitary(algorithm='orthonormal')
             Traceback (most recent call last):
             ...
@ -485,7 +530,7 @@ index 48e0a8a97f..1be5d35b19 100644
 
         TESTS::
 
-@@ -3662,8 +3662,8 @@ cdef class Matrix_double_dense(Matrix_dense):
+@@ -3635,8 +3636,8 @@ cdef class Matrix_double_dense(Matrix_dense):
             [0.0 1.0 2.0]
             [3.0 4.0 5.0]
             sage: m.numpy()
@ -496,7 +541,7 @@ index 48e0a8a97f..1be5d35b19 100644
 
         Alternatively, numpy automatically calls this function (via
         the magic :meth:`__array__` method) to convert Sage matrices
-@@ -3674,16 +3674,16 @@ cdef class Matrix_double_dense(Matrix_dense):
+@@ -3647,16 +3648,16 @@ cdef class Matrix_double_dense(Matrix_dense):
             [0.0 1.0 2.0]
             [3.0 4.0 5.0]
             sage: numpy.array(m)
@ -518,10 +563,10 @@ index 48e0a8a97f..1be5d35b19 100644
             dtype('complex128')
 
 diff --git a/src/sage/matrix/special.py b/src/sage/matrix/special.py
-index c698ba5e97..b743bab354 100644
+index ccbd208810..c3f9a65093 100644
 --- a/src/sage/matrix/special.py
 +++ b/src/sage/matrix/special.py
-@@ -705,7 +705,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True):
+@@ -706,7 +706,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True):
 
         sage: import numpy
         sage: entries = numpy.array([1.2, 5.6]); entries
@ -530,7 +575,7 @@ index c698ba5e97..b743bab354 100644
         sage: A = diagonal_matrix(3, entries); A
         [1.2 0.0 0.0]
         [0.0 5.6 0.0]
-@@ -715,7 +715,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True):
+@@ -716,7 +716,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True):
 
         sage: j = numpy.complex(0,1)
         sage: entries = numpy.array([2.0+j, 8.1, 3.4+2.6*j]); entries
@ -540,10 +585,10 @@ index c698ba5e97..b743bab354 100644
         [2.0 + 1.0*I         0.0         0.0]
         [        0.0         8.1         0.0]
 diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx
-index 230f142117..2ab1c0ae68 100644
+index 37d92c1282..955d083b34 100644
 --- a/src/sage/modules/free_module_element.pyx
 +++ b/src/sage/modules/free_module_element.pyx
-@@ -982,7 +982,7 @@ cdef class FreeModuleElement(Vector):   # abstract base class
+@@ -988,7 +988,7 @@ cdef class FreeModuleElement(Vector):   # abstract base class
             sage: v.numpy()
             array([1, 2, 5/6], dtype=object)
             sage: v.numpy(dtype=float)
@ -552,7 +597,7 @@ index 230f142117..2ab1c0ae68 100644
             sage: v.numpy(dtype=int)
             array([1, 2, 0])
             sage: import numpy
-@@ -993,7 +993,7 @@ cdef class FreeModuleElement(Vector):   # abstract base class
+@@ -999,7 +999,7 @@ cdef class FreeModuleElement(Vector):   # abstract base class
         be more efficient but may have unintended consequences::
 
             sage: v.numpy(dtype=None)
@ -596,22 +641,6 @@ index 39fc2970de..2badf98284 100644
         """
         if dtype is None or dtype is self._vector_numpy.dtype:
             from copy import copy
-diff --git a/src/sage/numerical/optimize.py b/src/sage/numerical/optimize.py
-index 17b5ebb84b..92ce35c502 100644
--- a/src/sage/numerical/optimize.py
-+++ b/src/sage/numerical/optimize.py
-@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args)
-                 else:
-                     min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0]
-         elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression):
-            min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args)
-+            min = optimize.fmin_cobyla(f, x0, cons, disp=0, **args)
-     elif isinstance(cons, function_type) or isinstance(cons, Expression):
-        min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args)
-+        min = optimize.fmin_cobyla(f, x0, cons, disp=0, **args)
-     return vector(RDF, min)
- 
- 
 diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx
 index ad9693da62..758fb709b7 100644
 --- a/src/sage/plot/complex_plot.pyx
@ -649,6 +678,76 @@ index ad9693da62..758fb709b7 100644
     """
     import numpy
     cdef unsigned int i, j, imax, jmax
+diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py
+index 5d28473731..fc4b2046c0 100644
+--- a/src/sage/plot/histogram.py
+++ b/src/sage/plot/histogram.py
+@@ -53,10 +53,17 @@ class Histogram(GraphicPrimitive):
+         """
+         import numpy as np
+         self.datalist=np.asarray(datalist,dtype=float)
+        if 'normed' in options:
+            from sage.misc.superseded import deprecation
+            deprecation(25260, "the 'normed' option is deprecated. Use 'density' instead.")
+         if 'linestyle' in options:
+             from sage.plot.misc import get_matplotlib_linestyle
+             options['linestyle'] = get_matplotlib_linestyle(
+                     options['linestyle'], return_type='long')
+        if options.get('range', None):
+            # numpy.histogram performs type checks on "range" so this must be
+            # actual floats
+            options['range'] = [float(x) for x in options['range']]
+         GraphicPrimitive.__init__(self, options)
+ 
+     def get_minmax_data(self):
+@@ -80,10 +87,14 @@ class Histogram(GraphicPrimitive):
+             {'xmax': 4.0, 'xmin': 0, 'ymax': 2, 'ymin': 0}
+ 
+         TESTS::
+-
+             sage: h = histogram([10,3,5], normed=True)[0]
+-            sage: h.get_minmax_data()  # rel tol 1e-15
+-            {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.4761904761904765, 'ymin': 0}
+            doctest:warning...:
+            DeprecationWarning: the 'normed' option is deprecated. Use 'density' instead.
+            See https://trac.sagemath.org/25260 for details.
+            sage: h.get_minmax_data()
+            doctest:warning ...:
+            VisibleDeprecationWarning: Passing `normed=True` on non-uniform bins has always been broken, and computes neither the probability density function nor the probability mass function. The result is only correct if the bins are uniform, when density=True will produce the same result anyway. The argument will be removed in a future version of numpy.
+            {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0}
+         """
+         import numpy
+ 
+@@ -152,7 +163,7 @@ class Histogram(GraphicPrimitive):
+                 'rwidth': 'The relative width of the bars as a fraction of the bin width',
+                 'cumulative': '(True or False) If True, then a histogram is computed in which each bin gives the counts in that bin plus all bins for smaller values.  Negative values give a reversed direction of accumulation.',
+                 'range': 'A list [min, max] which define the range of the histogram. Values outside of this range are treated as outliers and omitted from counts.',
+-                'normed': 'Deprecated alias for density',
+                'normed': 'Deprecated. Use density instead.',
+                 'density': '(True or False) If True, the counts are normalized to form a probability density. (n/(len(x)*dbin)',
+                 'weights': 'A sequence of weights the same length as the data list. If supplied, then each value contributes its associated weight to the bin count.',
+                 'stacked': '(True or False) If True, multiple data are stacked on top of each other.',
+@@ -199,7 +210,7 @@ class Histogram(GraphicPrimitive):
+             subplot.hist(self.datalist.transpose(), **options)
+ 
+ 
+-@options(aspect_ratio='automatic',align='mid', weights=None, range=None, bins=10, edgecolor='black')
+@options(aspect_ratio='automatic', align='mid', weights=None, range=None, bins=10, edgecolor='black')
+ def histogram(datalist, **options):
+     """
+     Computes and draws the histogram for list(s) of numerical data.
+@@ -231,8 +242,9 @@ def histogram(datalist, **options):
+     - ``linewidth`` -- (float) width of the lines defining the bars
+     - ``linestyle`` -- (default: 'solid') Style of the line. One of 'solid'
+       or '-', 'dashed' or '--', 'dotted' or ':', 'dashdot' or '-.'
+-    - ``density`` -- (boolean - default: False) If True, the counts are
+-      normalized to form a probability density.
+    - ``density`` -- (boolean - default: False) If True, the result is the
+      value of the probability density function at the bin, normalized such
+      that the integral over the range is 1.
+     - ``range`` -- A list [min, max] which define the range of the
+       histogram. Values outside of this range are treated as outliers and
+       omitted from counts
 diff --git a/src/sage/plot/line.py b/src/sage/plot/line.py
 index 23f5e61446..3b1b51d7cf 100644
 --- a/src/sage/plot/line.py
@ -718,7 +817,7 @@ index f3da57c370..3806f4b32f 100644
         TESTS:
 
 diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx
-index f66cd898b9..35995886d5 100644
+index 1b119e323f..3290b00695 100644
 --- a/src/sage/probability/probability_distribution.pyx
 +++ b/src/sage/probability/probability_distribution.pyx
@@ -130,7 +130,17 @@ cdef class ProbabilityDistribution:
@ -741,10 +840,10 @@ index f66cd898b9..35995886d5 100644
         import pylab
         l = [float(self.get_random_element()) for _ in range(num_samples)]
 diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx
-index a0bfe080f5..7d95e7a1a8 100644
+index 12ca1b222b..9bad7dae0c 100644
 --- a/src/sage/rings/rational.pyx
 +++ b/src/sage/rings/rational.pyx
-@@ -1056,7 +1056,7 @@ cdef class Rational(sage.structure.element.FieldElement):
+@@ -1041,7 +1041,7 @@ cdef class Rational(sage.structure.element.FieldElement):
             dtype('O')
 
             sage: numpy.array([1, 1/2, 3/4])
@ -754,10 +853,10 @@ index a0bfe080f5..7d95e7a1a8 100644
         if mpz_cmp_ui(mpq_denref(self.value), 1) == 0:
             if mpz_fits_slong_p(mpq_numref(self.value)):
 diff --git a/src/sage/rings/real_mpfr.pyx b/src/sage/rings/real_mpfr.pyx
-index 4c630867a4..64e2187f5b 100644
+index 9b90c8833e..1ce05b937d 100644
 --- a/src/sage/rings/real_mpfr.pyx
 +++ b/src/sage/rings/real_mpfr.pyx
-@@ -1438,7 +1438,7 @@ cdef class RealNumber(sage.structure.element.RingElement):
+@@ -1439,7 +1439,7 @@ cdef class RealNumber(sage.structure.element.RingElement):
 
             sage: import numpy
             sage: numpy.arange(10.0)
@ -767,10 +866,10 @@ index 4c630867a4..64e2187f5b 100644
             dtype('float64')
             sage: numpy.array([1.000000000000000000000000000000000000]).dtype
 diff --git a/src/sage/schemes/elliptic_curves/height.py b/src/sage/schemes/elliptic_curves/height.py
-index 3d270ebf9d..1144f168e3 100644
+index de31fe9883..7a33ea6f5b 100644
 --- a/src/sage/schemes/elliptic_curves/height.py
 +++ b/src/sage/schemes/elliptic_curves/height.py
-@@ -1623,18 +1623,18 @@ class EllipticCurveCanonicalHeight:
+@@ -1627,18 +1627,18 @@ class EllipticCurveCanonicalHeight:
         even::
 
             sage: H.wp_on_grid(v,4)
@ -798,10 +897,10 @@ index 3d270ebf9d..1144f168e3 100644
         tau = self.tau(v)
         fk, err = self.fk_intervals(v, 15, CDF)
 diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx
-index 2dcb0492b9..2b1a06385c 100644
+index 9da38002e8..d61e74bf82 100644
 --- a/src/sage/symbolic/ring.pyx
 +++ b/src/sage/symbolic/ring.pyx
-@@ -1135,7 +1135,7 @@ cdef class NumpyToSRMorphism(Morphism):
+@@ -1136,7 +1136,7 @@ cdef class NumpyToSRMorphism(Morphism):
         sage: cos(numpy.int('2'))
         cos(2)
         sage: numpy.cos(numpy.int('2'))
--- a/pkgs/applications/science/math/sage/sage-env.nix
+++ b/pkgs/applications/science/math/sage/sage-env.nix
@ -37,7 +37,7 @@
 , lcalc
 , rubiks
 , flintqs
-, openblasCompat
+, openblas-cblas-pc
 , flint
 , gmp
 , mpfr
@ -98,9 +98,9 @@ writeTextFile rec {
    export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [
        # This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case
        # for it outside of the tests. However since singular and openblas are runtime dependencies anyways
-        # it doesn't really hurt to include.
+        # and openblas-cblas-pc is tiny, it doesn't really hurt to include.
        singular
-        openblasCompat
+        openblas-cblas-pc
      ])
    }'
    export SAGE_ROOT='${sage-src}'
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@ -94,9 +94,20 @@ stdenv.mkDerivation rec {
      stripLen = 1;
    })

-    # Only formatting changes.
+    (fetchpatch {
+      name = "matplotlib-2.2.2";
+      url = "https://git.sagemath.org/sage.git/patch?id=0d6244ed53b71aba861ce3d683d33e542c0bf0b0";
+      sha256 = "15x4cadxxlsdfh2sblgagqjj6ir13fgdzixxnwnvzln60saahb34";
+    })
+
+    (fetchpatch {
+      name = "scipy-1.1.0";
+      url = "https://git.sagemath.org/sage.git/patch?id=e0db968a51678b34ebd8d34906c7042900272378";
+      sha256 = "0kq5zxqphhrmavrmg830wdr7hwp1bkzdqlf3jfqfr8r8xq12qwf7";
+    })
+
    # https://trac.sagemath.org/ticket/25260
-    ./patches/numpy-1.14.3.patch
+    ./patches/numpy-1.15.1.patch

    # https://trac.sagemath.org/ticket/25862
    ./patches/eclib-20180710.patch
--- a/pkgs/applications/science/math/sage/sage-with-env.nix
+++ b/pkgs/applications/science/math/sage/sage-with-env.nix
@ -4,6 +4,9 @@
 , sage-env
 , sage-src
 , openblasCompat
+, openblas-blas-pc
+, openblas-cblas-pc
+, openblas-lapack-pc
 , pkg-config
 , three
 , singular
@ -29,6 +32,9 @@ let
    makeWrapper
    pkg-config
    openblasCompat # lots of segfaults with regular (64 bit) openblas
+    openblas-blas-pc
+    openblas-cblas-pc
+    openblas-lapack-pc
    singular
    three
    pynac
--- a/pkgs/applications/science/math/sage/sagelib.nix
+++ b/pkgs/applications/science/math/sage/sagelib.nix
@ -3,6 +3,9 @@
 , buildPythonPackage
 , arb
 , openblasCompat
+, openblas-blas-pc
+, openblas-cblas-pc
+, openblas-lapack-pc
 , brial
 , cliquer
 , cypari2
@ -56,7 +59,9 @@ buildPythonPackage rec {
  nativeBuildInputs = [
    iml
    perl
-    openblasCompat
+    openblas-blas-pc
+    openblas-cblas-pc
+    openblas-lapack-pc
    jupyter_core
  ];

--- a/pkgs/applications/science/misc/root/default.nix
+++ b/pkgs/applications/science/misc/root/default.nix
@ -67,10 +67,11 @@ stdenv.mkDerivation rec {

  setupHook = ./setup-hook.sh;

-  meta = {
+  meta = with stdenv.lib; {
    homepage = https://root.cern.ch/;
    description = "A data analysis framework";
-    platforms = stdenv.lib.platforms.unix;
-    maintainers = with stdenv.lib.maintainers; [ veprbl ];
+    platforms = platforms.unix;
+    maintainers = [ maintainers.veprbl ];
+    license = licenses.lgpl21;
  };
 }
--- a/pkgs/applications/version-management/bazaar/default.nix
+++ b/pkgs/applications/version-management/bazaar/default.nix
@ -27,9 +27,10 @@ python2Packages.buildPythonApplication rec {
      --subst-var-by certPath /etc/ssl/certs/ca-certificates.crt
  '';

-  meta = {
+  meta = with stdenv.lib; {
    homepage = http://bazaar-vcs.org/;
    description = "A distributed version control system that Just Works";
-    platforms = stdenv.lib.platforms.unix;
+    platforms = platforms.unix;
+    license = licenses.gpl2Plus;
  };
 }
--- a/Show More
+++ b/Show More