Merge commit 'master' into staging

2018-08-02 16:13:33 -04:00 · 2018-08-02 16:13:33 -04:00 · 89c21fce3f
commit 89c21fce3f
parent b9fbcfb487 89a89ddfb3
97 changed files with 3249 additions and 657 deletions
--- a/README.md
+++ b/README.md
@ -37,5 +37,6 @@ For pull-requests, please rebase onto nixpkgs `master`.

 Communication:

+* [Discourse Forum](https://discourse.nixos.org/)
 * [Mailing list](https://groups.google.com/forum/#!forum/nix-devel)
 * [IRC - #nixos on freenode.net](irc://irc.freenode.net/#nixos)
--- a/doc/platform-notes.xml
+++ b/doc/platform-notes.xml
@ -29,6 +29,7 @@
      }
    </programlisting>
   </listitem>
+
   <listitem>
    <para>
     On darwin libraries are linked using absolute paths, libraries are
@ -46,6 +47,37 @@
      }
    </programlisting>
   </listitem>
+
+   <listitem>
+    <para>
+     Even if the libraries are linked using absolute paths and resolved via
+     their <literal>install_name</literal> correctly, tests can sometimes fail
+     to run binaries.  This happens because the <varname>checkPhase</varname>
+     runs before the libraries are installed.
+    </para>
+    <para>
+     This can usually be solved by running the tests after the
+     <varname>installPhase</varname> or alternatively by using
+     <varname>DYLD_LIBRARY_PATH</varname>. More information about this variable
+     can be found in the <citerefentry><refentrytitle>dyld</refentrytitle>
+     <manvolnum>1</manvolnum></citerefentry> manpage.
+    </para>
+<programlisting>
+      dyld: Library not loaded: /nix/store/7hnmbscpayxzxrixrgxvvlifzlxdsdir-jq-1.5-lib/lib/libjq.1.dylib
+      Referenced from: /private/tmp/nix-build-jq-1.5.drv-0/jq-1.5/tests/../jq
+      Reason: image not found
+      ./tests/jqtest: line 5: 75779 Abort trap: 6
+    </programlisting>
+<programlisting>
+      stdenv.mkDerivation {
+        name = "libfoo-1.2.3";
+        # ...
+        doInstallCheck = true;
+        installCheckTarget = "check";
+      }
+    </programlisting>
+   </listitem>
+
   <listitem>
    <para>
     Some packages assume xcode is available and use <command>xcrun</command>
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@ -3197,6 +3197,11 @@
    email = "patrick.callahan@latitudeengineering.com";
    name = "Patrick Callahan";
  };
+  q3k = {
+    email = "q3k@q3k.org";
+    github = "q3k";
+    name = "Serge Bazanski";
+  };
  qknight = {
    email = "js@lastlog.de";
    github = "qknight";
--- a/nixos/doc/manual/release-notes/rl-1809.xml
+++ b/nixos/doc/manual/release-notes/rl-1809.xml
@ -370,7 +370,12 @@ inherit (pkgs.nixos {
      <varname>s6-dns</varname>, <varname>s6-networking</varname>,
      <varname>s6-linux-utils</varname> and <varname>s6-portable-utils</varname> respectively.
    </para>
-   </listitem>
+  </listitem>
+  <listitem>
+    <para>
+      The module option <option>nix.useSandbox</option> is now defaulted to <literal>true</literal>.
+    </para>
+  </listitem>
  </itemizedlist>
 </section>
 </section>
--- a/nixos/modules/module-list.nix
+++ b/nixos/modules/module-list.nix
@ -543,6 +543,7 @@
  ./services/networking/ntopng.nix
  ./services/networking/ntpd.nix
  ./services/networking/nylon.nix
+  ./services/networking/ocserv.nix
  ./services/networking/oidentd.nix
  ./services/networking/openfire.nix
  ./services/networking/openntpd.nix
--- a/nixos/modules/services/backup/restic.nix
+++ b/nixos/modules/services/backup/restic.nix
@ -18,6 +18,7 @@ with lib;

        s3CredentialsFile = mkOption {
          type = with types; nullOr str;
+          default = null;
          description = ''
            file containing the AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY
            for an S3-hosted repository, in the format of an EnvironmentFile
--- a/nixos/modules/services/misc/nix-daemon.nix
+++ b/nixos/modules/services/misc/nix-daemon.nix
@ -127,16 +127,16 @@ in

      useSandbox = mkOption {
        type = types.either types.bool (types.enum ["relaxed"]);
-        default = false;
+        default = true;
        description = "
          If set, Nix will perform builds in a sandboxed environment that it
          will set up automatically for each build. This prevents impurities
          in builds by disallowing access to dependencies outside of the Nix
          store by using network and mount namespaces in a chroot environment.
-          This isn't enabled by default for possible performance impacts due to
-          the initial setup time of a sandbox for each build. It doesn't affect
-          derivation hashes, so changing this option will not trigger a rebuild
-          of packages.
+          This is enabled by default even though it has a possible performance
+          impact due to the initial setup time of a sandbox for each build. It
+          doesn't affect derivation hashes, so changing this option will not
+          trigger a rebuild of packages.
        ";
      };

--- a/nixos/modules/services/monitoring/graphite.nix
+++ b/nixos/modules/services/monitoring/graphite.nix
@ -136,7 +136,7 @@ in {
      finders = mkOption {
        description = "List of finder plugins to load.";
        default = [];
-        example = literalExample "[ pkgs.python27Packages.graphite_influxdb ]";
+        example = literalExample "[ pkgs.python27Packages.influxgraph ]";
        type = types.listOf types.package;
      };

@ -485,7 +485,7 @@ in {
          PYTHONPATH = let
              penv = pkgs.python.buildEnv.override {
                extraLibs = [
-                  pythonPackages.graphite_web
+                  pythonPackages.graphite-web
                  pythonPackages.pysqlite
                ];
              };
@ -524,16 +524,16 @@ in {
          fi

          # Only collect static files when graphite_web changes.
-          if ! [ "${dataDir}/current_graphite_web" -ef "${pythonPackages.graphite_web}" ]; then
+          if ! [ "${dataDir}/current_graphite_web" -ef "${pythonPackages.graphite-web}" ]; then
            mkdir -p ${staticDir}
            ${pkgs.pythonPackages.django_1_8}/bin/django-admin.py collectstatic  --noinput --clear
            chown -R graphite:graphite ${staticDir}
-            ln -sfT "${pythonPackages.graphite_web}" "${dataDir}/current_graphite_web"
+            ln -sfT "${pythonPackages.graphite-web}" "${dataDir}/current_graphite_web"
          fi
        '';
      };

-      environment.systemPackages = [ pythonPackages.graphite_web ];
+      environment.systemPackages = [ pythonPackages.graphite-web ];
    }))

    (mkIf cfg.api.enable {
@ -607,7 +607,7 @@ in {
          GRAPHITE_URL = cfg.pager.graphiteUrl;
        };
        serviceConfig = {
-          ExecStart = "${pkgs.pythonPackages.graphite_pager}/bin/graphite-pager --config ${pagerConfig}";
+          ExecStart = "${pkgs.pythonPackages.graphitepager}/bin/graphite-pager --config ${pagerConfig}";
          User = "graphite";
          Group = "graphite";
        };
@ -615,7 +615,7 @@ in {

      services.redis.enable = mkDefault true;

-      environment.systemPackages = [ pkgs.pythonPackages.graphite_pager ];
+      environment.systemPackages = [ pkgs.pythonPackages.graphitepager ];
    })

    (mkIf cfg.beacon.enable {
--- a/nixos/modules/services/networking/ocserv.nix
+++ b/nixos/modules/services/networking/ocserv.nix
@ -0,0 +1,99 @@
+{ config, pkgs, lib, ... }:
+
+with lib;
+
+let
+
+  cfg = config.services.ocserv;
+
+in
+
+{
+  options.services.ocserv = {
+    enable = mkEnableOption "ocserv";
+
+    config = mkOption {
+      type = types.lines;
+
+      description = ''
+        Configuration content to start an OCServ server.
+
+        For a full configuration reference,please refer to the online documentation
+        (https://ocserv.gitlab.io/www/manual.html), the openconnect
+        recipes (https://github.com/openconnect/recipes) or `man ocserv`.
+      '';
+
+      example = ''
+        # configuration examples from $out/doc without explanatory comments.
+        # for a full reference please look at the installed man pages.
+        auth = "plain[passwd=./sample.passwd]"
+        tcp-port = 443
+        udp-port = 443
+        run-as-user = nobody
+        run-as-group = nogroup
+        socket-file = /var/run/ocserv-socket
+        server-cert = certs/server-cert.pem
+        server-key = certs/server-key.pem
+        keepalive = 32400
+        dpd = 90
+        mobile-dpd = 1800
+        switch-to-tcp-timeout = 25
+        try-mtu-discovery = false
+        cert-user-oid = 0.9.2342.19200300.100.1.1
+        tls-priorities = "NORMAL:%SERVER_PRECEDENCE:%COMPAT:-VERS-SSL3.0"
+        auth-timeout = 240
+        min-reauth-time = 300
+        max-ban-score = 80
+        ban-reset-time = 1200
+        cookie-timeout = 300
+        deny-roaming = false
+        rekey-time = 172800
+        rekey-method = ssl
+        use-occtl = true
+        pid-file = /var/run/ocserv.pid
+        device = vpns
+        predictable-ips = true
+        default-domain = example.com
+        ipv4-network = 192.168.1.0
+        ipv4-netmask = 255.255.255.0
+        dns = 192.168.1.2
+        ping-leases = false
+        route = 10.10.10.0/255.255.255.0
+        route = 192.168.0.0/255.255.0.0
+        no-route = 192.168.5.0/255.255.255.0
+        cisco-client-compat = true
+        dtls-legacy = true
+
+        [vhost:www.example.com]
+        auth = "certificate"
+        ca-cert = certs/ca.pem
+        server-cert = certs/server-cert-secp521r1.pem
+        server-key = cersts/certs/server-key-secp521r1.pem
+        ipv4-network = 192.168.2.0
+        ipv4-netmask = 255.255.255.0
+        cert-user-oid = 0.9.2342.19200300.100.1.1
+      '';
+    };
+  };
+
+  config = mkIf cfg.enable {
+    environment.systemPackages = [ pkgs.ocserv ];
+    environment.etc."ocserv/ocserv.conf".text = cfg.config;
+
+    security.pam.services.ocserv = {};
+
+    systemd.services.ocserv = {
+      description = "OpenConnect SSL VPN server";
+      documentation = [ "man:ocserv(8)" ];
+      after = [ "dbus.service" "network-online.target" ];
+      wantedBy = [ "multi-user.target" ];
+
+      serviceConfig = {
+        PrivateTmp = true;
+        PIDFile = "/var/run/ocserv.pid";
+        ExecStart = "${pkgs.ocserv}/bin/ocserv --foreground --pid-file /var/run/ocesrv.pid --config /etc/ocserv/ocserv.conf";
+        ExecReload = "${pkgs.coreutils}/bin/kill -HUP $MAINPID";
+      };
+    };
+  };
+}
--- a/nixos/tests/containers-imperative.nix
+++ b/nixos/tests/containers-imperative.nix
@ -9,6 +9,11 @@ import ./make-test.nix ({ pkgs, ...} : {
  machine =
    { config, pkgs, lib, ... }:
    { imports = [ ../modules/installer/cd-dvd/channel.nix ];
+
+      # XXX: Sandbox setup fails while trying to hardlink files from the host's
+      #      store file system into the prepared chroot directory.
+      nix.useSandbox = false;
+
      virtualisation.writableStore = true;
      virtualisation.memorySize = 1024;
      # Make sure we always have all the required dependencies for creating a
--- a/nixos/tests/graphite.nix
+++ b/nixos/tests/graphite.nix
@ -1,4 +1,4 @@
-import ./make-test.nix ({ ... } :
+import ./make-test.nix ({ pkgs, ... } :
 {
  name = "graphite";
  nodes = {
@ -11,10 +11,12 @@ import ./make-test.nix ({ ... } :
          api = {
            enable = true;
            port = 8082;
+            finders = [ pkgs.python27Packages.influxgraph ];
          };
          carbon.enableCache = true;
          seyren.enable = true;
          pager.enable = true;
+          beacon.enable = true;
        };
      };
  };
@ -25,6 +27,7 @@ import ./make-test.nix ({ ... } :
    $one->waitForUnit("graphiteWeb.service");
    $one->waitForUnit("graphiteApi.service");
    $one->waitForUnit("graphitePager.service");
+    $one->waitForUnit("graphite-beacon.service");
    $one->waitForUnit("carbonCache.service");
    $one->waitForUnit("seyren.service");
    # The services above are of type "simple". systemd considers them active immediately
--- a/pkgs/applications/editors/android-studio/common.nix
+++ b/pkgs/applications/editors/android-studio/common.nix
@ -1,4 +1,5 @@
-{ pname, version, build, sha256Hash, meta }:
+{ channel, pname, version, build, sha256Hash }:
+
 { bash
 , buildFHSUserEnv
 , coreutils
@ -36,8 +37,9 @@
 }:

 let
+  drvName = "android-studio-${channel}-${version}";
  androidStudio = stdenv.mkDerivation {
-    name = "${pname}-${version}";
+    name = drvName;

    src = fetchurl {
      url = "https://dl.google.com/dl/android/studio/ide-zips/${version}/android-studio-ide-${build}-linux.zip";
@ -115,17 +117,32 @@ let
  # (e.g. `mksdcard`) have `/lib/ld-linux.so.2` set as the interpreter. An FHS
  # environment is used as a work around for that.
  fhsEnv = buildFHSUserEnv {
-    name = "${pname}-fhs-env";
+    name = "${drvName}-fhs-env";
    multiPkgs = pkgs: [ pkgs.ncurses5 ];
  };

 in
  writeTextFile {
-    name = "${pname}-${version}";
+    name = "${drvName}-wrapper";
+    # TODO: Rename preview -> beta (and add -stable suffix?):
    destination = "/bin/${pname}";
    executable = true;
    text = ''
      #!${bash}/bin/bash
-      ${fhsEnv}/bin/${pname}-fhs-env ${androidStudio}/bin/studio.sh
+      ${fhsEnv}/bin/${drvName}-fhs-env ${androidStudio}/bin/studio.sh
    '';
-  } // { inherit meta; }
+  } // {
+    meta = with stdenv.lib; {
+      description = "The Official IDE for Android (${channel} channel)";
+      longDescription = ''
+        Android Studio is the official IDE for Android app development, based on
+        IntelliJ IDEA.
+      '';
+      homepage = if channel == "stable"
+        then https://developer.android.com/studio/index.html
+        else https://developer.android.com/studio/preview/index.html;
+      license = licenses.asl20;
+      platforms = [ "x86_64-linux" ];
+      maintainers = with maintainers; [ primeos ];
+    };
+  }
--- a/pkgs/applications/editors/android-studio/default.nix
+++ b/pkgs/applications/editors/android-studio/default.nix
@ -12,7 +12,12 @@ let
    build = "173.4819257";
    sha256Hash = "196yaswbxh2nd83gimjxr8ggr5xkdxq7n3xlh6ax73v59pj4hryq";
  };
-  latestVersion = {
+  betaVersion = {
+    version = "3.2.0.22"; # "Android Studio 3.2 Beta 5"
+    build = "181.4913314";
+    sha256Hash = "016nyn1pqviy089hg0dq7m4cqb39fdxdcy4zknkaq7dmgv1dj6x9";
+  };
+  latestVersion = { # canary & dev
    version = "3.3.0.2"; # "Android Studio 3.3 Canary 3"
    build = "181.4884283";
    sha256Hash = "0r93yzw87cgzz60p60gknij5vaqmv1a1kyd4cr9gx8cbxw46lhwh";
@ -21,51 +26,25 @@ in rec {
  # Old alias
  preview = beta;

-  # Attributes are named by the corresponding release channels
+  # Attributes are named by their corresponding release channels

  stable = mkStudio (stableVersion // {
+    channel = "stable";
    pname = "android-studio";
-    #pname = "android-studio-stable"; # TODO: Rename and provide symlink
-
-    meta = with stdenv.lib; {
-      description = "The Official IDE for Android (stable channel)";
-      longDescription = ''
-        Android Studio is the official IDE for Android app development, based on
-        IntelliJ IDEA.
-      '';
-      homepage = https://developer.android.com/studio/index.html;
-      license = licenses.asl20;
-      platforms = [ "x86_64-linux" ];
-      maintainers = with maintainers; [ primeos ];
-    };
  });

-  beta = mkStudio (latestVersion // {
+  beta = mkStudio (betaVersion // {
+    channel = "beta";
    pname = "android-studio-preview";
-    #pname = "android-studio-beta"; # TODO: Rename and provide symlink
-    version = "3.2.0.22"; # "Android Studio 3.2 Beta 5"
-    build = "181.4913314";
-    sha256Hash = "016nyn1pqviy089hg0dq7m4cqb39fdxdcy4zknkaq7dmgv1dj6x9";
-
-    meta = stable.meta // {
-      description = "The Official IDE for Android (beta channel)";
-      homepage = https://developer.android.com/studio/preview/index.html;
-    };
  });

  dev = mkStudio (latestVersion // {
+    channel = "dev";
    pname = "android-studio-dev";
-
-    meta = beta.meta // {
-      description = "The Official IDE for Android (dev channel)";
-    };
  });

  canary = mkStudio (latestVersion // {
+    channel = "canary";
    pname = "android-studio-canary";
-
-    meta = beta.meta // {
-      description = "The Official IDE for Android (canary channel)";
-    };
  });
 }
--- a/pkgs/applications/editors/gnome-builder/default.nix
+++ b/pkgs/applications/editors/gnome-builder/default.nix
@ -0,0 +1,155 @@
+{ stdenv
+, desktop-file-utils
+, docbook_xsl
+, docbook_xml_dtd_43
+, fetchpatch
+, fetchurl
+, flatpak
+, glibcLocales
+, gnome3
+, gobjectIntrospection
+, gspell
+, gtk-doc
+, gtk3
+, gtksourceview3
+, hicolor-icon-theme
+, json-glib
+, jsonrpc-glib
+, libdazzle
+, libxml2
+, meson
+, ninja
+, ostree
+, pcre
+, pkgconfig
+, python3
+, sysprof
+, template-glib
+, vala
+, webkitgtk
+, wrapGAppsHook
+}:
+let
+  version = "3.28.4";
+  pname = "gnome-builder";
+in stdenv.mkDerivation {
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://gnome/sources/${pname}/${gnome3.versionBranch version}/${pname}-${version}.tar.xz";
+    sha256 = "0ibb74jlyrl5f6rj1b74196zfg2qaf870lxgi76qzpkgwq0iya05";
+  };
+
+  nativeBuildInputs = [
+    #appstream-glib # tests fail if these tools are available
+    desktop-file-utils
+    docbook_xsl
+    docbook_xml_dtd_43
+    glibcLocales # for Meson's gtkdochelper
+    gobjectIntrospection
+    gtk-doc
+    hicolor-icon-theme
+    meson
+    ninja
+    pkgconfig
+    python3.pkgs.wrapPython
+    wrapGAppsHook
+  ];
+
+  buildInputs = [
+    flatpak
+    gnome3.devhelp
+    gnome3.libgit2-glib
+    gnome3.libpeas
+    gnome3.vte
+    gspell
+    gtk3
+    gtksourceview3
+    json-glib
+    jsonrpc-glib
+    libdazzle
+    libxml2
+    ostree
+    pcre
+    python3
+    sysprof
+    template-glib
+    vala
+    webkitgtk
+  ];
+
+  outputs = [ "out" "devdoc" ];
+
+  prePatch = ''
+    patchShebangs build-aux/meson/post_install.py
+  '';
+
+  patches = [
+    (fetchpatch {
+      name = "absolute-shared-library-path.patch";
+      url = "https://gitlab.gnome.org/GNOME/gnome-builder/commit/1011cabc519fd7322e2d695c79bfce3e18ff6200.patch";
+      sha256 = "1g12zziidzrphp527aa8sklfaln4qpjprkz73f0c9w5ph6k252fw";
+    })
+    (fetchpatch {
+      name = "python-libprefix.patch";
+      url = "https://gitlab.gnome.org/GNOME/gnome-builder/commit/43494ce83a347f369ed4cfb8dd71d3b93452736b.patch";
+      sha256 = "0kgi3n3g13n1j4xa61ln9xiahcfdc43bxi5mw4yva2d5px445msf";
+    })
+    (fetchpatch {
+      name = "ostree-dependency.patch";
+      url = "https://gitlab.gnome.org/GNOME/gnome-builder/commit/8b11773b65c95f464a0de16b91318c1ca73deeae.patch";
+      sha256 = "18r4hd90id0w6r0lzqpw83bcj45nm9jhr46a0ffi1mcayb18mgbk";
+    })
+  ];
+
+  mesonFlags = [
+    "-Dpython_libprefix=${python3.libPrefix}"
+    "-Dwith_docs=true"
+
+    # Making the build system correctly detect clang header and library paths
+    # is difficult. Somebody should look into fixing this.
+    "-Dwith_clang=false"
+  ];
+
+  # Some tests fail due to being unable to find the Vte typelib, and I don't
+  # understand why. Somebody should look into fixing this.
+  doCheck = false;
+
+  preInstall = ''
+    export LC_ALL="en_US.utf-8"
+  '';
+
+  pythonPath = with python3.pkgs; requiredPythonModules [ pygobject3 ];
+
+  preFixup = ''
+    buildPythonPath "$out $pythonPath"
+    gappsWrapperArgs+=(
+      --prefix PYTHONPATH : "$program_PYTHONPATH"
+    )
+
+    # Ensure that all plugins get their interpreter paths fixed up.
+    find $out/lib -name \*.py -type f -print0 | while read -d "" f; do
+      chmod a+x "$f"
+    done
+  '';
+
+  passthru.updateScript = gnome3.updateScript { packageName = pname; };
+
+  meta = with stdenv.lib; {
+    description = "An IDE for writing GNOME-based software";
+    longDescription = ''
+      Global search, auto-completion, source code map, documentation
+      reference, and other features expected in an IDE, but with a focus
+      on streamlining GNOME-based development projects.
+
+      This package does not pull in the dependencies needed for every
+      plugin. If you find that a plugin you wish to use doesn't work, we
+      currently recommend running gnome-builder inside a nix-shell with
+      appropriate dependencies loaded.
+    '';
+    homepage = https://wiki.gnome.org/Apps/Builder;
+    license = licenses.gpl3Plus;
+    maintainers = gnome3.maintainers;
+    platforms = platforms.linux;
+  };
+}
--- a/pkgs/applications/misc/doing/Gemfile
+++ b/pkgs/applications/misc/doing/Gemfile
@ -0,0 +1,2 @@
+source 'https://rubygems.org'
+gem 'doing', '1.0.10pre'
--- a/pkgs/applications/misc/doing/Gemfile.lock
+++ b/pkgs/applications/misc/doing/Gemfile.lock
@ -0,0 +1,25 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    chronic (0.10.2)
+    deep_merge (1.2.1)
+    doing (1.0.10pre)
+      chronic (~> 0.10, >= 0.10.2)
+      deep_merge
+      gli (~> 2.17.1)
+      haml (= 4.0.3)
+      json (~> 1.8.1)
+    gli (2.17.1)
+    haml (4.0.3)
+      tilt
+    json (1.8.6)
+    tilt (2.0.8)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  doing (= 1.0.10pre)
+
+BUNDLED WITH
+   1.14.6
--- a/pkgs/applications/misc/doing/default.nix
+++ b/pkgs/applications/misc/doing/default.nix
@ -0,0 +1,25 @@
+{ lib, bundlerEnv, ruby
+}:
+
+# Bundix:
+# nix-shell -p bundix zlib
+bundlerEnv rec {
+  pname = "doing";
+  version = (import ./gemset.nix).doing.version;
+
+  inherit ruby;
+  gemdir = ./.;
+
+  meta = with lib; {
+    description = "A command line tool for keeping track of what you’re doing and tracking what you’ve done.";
+    longDescription = ''
+      doing is a basic CLI for adding and listing "what was I doing" reminders
+      in a TaskPaper-formatted text file. It allows for multiple
+      sections/categories and flexible output formatting.
+    '';
+    homepage    = http://brettterpstra.com/projects/doing/;
+    license     = licenses.mit;
+    maintainers = with maintainers; [ ktf ];
+    platforms   = platforms.unix;
+  };
+}
--- a/pkgs/applications/misc/doing/gemset.nix
+++ b/pkgs/applications/misc/doing/gemset.nix
@ -0,0 +1,60 @@
+{
+  chronic = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1hrdkn4g8x7dlzxwb1rfgr8kw3bp4ywg5l4y4i9c2g5cwv62yvvn";
+      type = "gem";
+    };
+    version = "0.10.2";
+  };
+  deep_merge = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1q3picw7zx1xdkybmrnhmk2hycxzaa0jv4gqrby1s90dy5n7fmsb";
+      type = "gem";
+    };
+    version = "1.2.1";
+  };
+  doing = {
+    dependencies = ["chronic" "deep_merge" "gli" "haml" "json"];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1y42yc7h45sz9hqj3g1dd77ipx58l7v64i7mrsj3is2f5rszd1rv";
+      type = "gem";
+    };
+    version = "1.0.10pre";
+  };
+  gli = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0g7g3lxhh2b4h4im58zywj9vcfixfgndfsvp84cr3x67b5zm4kaq";
+      type = "gem";
+    };
+    version = "2.17.1";
+  };
+  haml = {
+    dependencies = ["tilt"];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1l9zhfdk9z7xjfdp108r9fw4xa55hflin7hh3lpafbf9bdz96knr";
+      type = "gem";
+    };
+    version = "4.0.3";
+  };
+  json = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0qmj7fypgb9vag723w1a49qihxrcf5shzars106ynw2zk352gbv5";
+      type = "gem";
+    };
+    version = "1.8.6";
+  };
+  tilt = {
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0020mrgdf11q23hm1ddd6fv691l51vi10af00f137ilcdb2ycfra";
+      type = "gem";
+    };
+    version = "2.0.8";
+  };
+}
--- a/pkgs/applications/misc/masterpdfeditor/default.nix
+++ b/pkgs/applications/misc/masterpdfeditor/default.nix
@ -4,7 +4,7 @@ let
 in stdenv.mkDerivation {
  name = "masterpdfeditor-${version}";
  src = fetchurl {
-    url = "https://get.code-industry.net/public/master-pdf-editor-${version}_qt5.amd64.tar.gz";
+    url = "https://code-industry.net/public/master-pdf-editor-${version}_qt5.amd64.tar.gz";
    sha256 = "0k5bzlhqglskiiq86nmy18mnh5bf2w3mr9cq3pibrwn5pisxnxxc";
  };

--- a/pkgs/applications/misc/xca/default.nix
+++ b/pkgs/applications/misc/xca/default.nix
@ -3,13 +3,13 @@

 mkDerivation rec {
  name = "xca-${version}";
-  version = "2.0.1";
+  version = "2.1.0";

  src = fetchFromGitHub {
    owner  = "chris2511";
    repo   = "xca";
    rev    = "RELEASE.${version}";
-    sha256 = "0906xnmqzd9q5irxzm19361vhzig9yqsmf6wsc3rggniix5bk3a8";
+    sha256 = "039qz6hh43hx8dcw2bq71mgy95zk09jyd3xxpldmxxd5d69zcr8m";
  };

  postPatch = ''
@ -23,8 +23,6 @@ mkDerivation rec {

  enableParallelBuilding = true;

-  configureFlags = [ "CXXFLAGS=-std=c++11" ];
-
  meta = with lib; {
    description = "Interface for managing asymetric keys like RSA or DSA";
    homepage    = http://xca.sourceforge.net/;
--- a/pkgs/applications/networking/instant-messengers/gitter/default.nix
+++ b/pkgs/applications/networking/instant-messengers/gitter/default.nix
@ -0,0 +1,71 @@
+{ stdenv, alsaLib, atk, cairo, cups, dbus, dpkg, expat, fetchurl
+, fontconfig, freetype, gdk_pixbuf, glib, gnome2, gtk3, libX11
+, libXScrnSaver, libXcomposite, libXcursor, libXdamage, libXext, libXfixes
+, libXi, libXrandr, libXrender, libXtst, libappindicator-gtk3, libcxx
+, libnotify, libpulseaudio, libxcb, makeDesktopItem, makeWrapper, nspr, nss
+, nwjs, pango, systemd }:
+
+let gitterDirectorySuffix = "opt/gitter";
+    doELFPatch = target: ''
+      patchelf --set-interpreter ${stdenv.cc.bintools.dynamicLinker} \
+         --set-rpath "$out/${gitterDirectorySuffix}/lib:${libPath}" \
+         $out/${gitterDirectorySuffix}/${target}
+       '';
+   libPath = stdenv.lib.makeLibraryPath [
+     alsaLib atk cairo cups dbus expat fontconfig freetype gdk_pixbuf glib
+     gnome2.GConf gtk3 libX11 libXScrnSaver libXcomposite libXcursor libXdamage
+     libXext libXfixes libXi libXrandr libXrender libXtst libappindicator-gtk3
+     libcxx libnotify libpulseaudio libxcb nspr nss pango stdenv.cc.cc systemd
+  ];
+in stdenv.mkDerivation rec {
+  pname = "gitter";
+  version = "4.1.0";
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "https://update.gitter.im/linux64/${pname}_${version}_amd64.deb";
+    sha256 = "1gny9i2pywvczzrs93k8krqn6hwm6c2zg8yr3xmjqs3p88817wbi";
+  };
+
+  nativeBuildInputs = [ makeWrapper dpkg ];
+
+  unpackPhase = "dpkg -x $src .";
+
+  installPhase = ''
+    mkdir -p $out/{bin,opt/gitter,share/pixmaps}
+    mv ./opt/Gitter/linux64/* $out/opt/gitter
+
+    ${doELFPatch "Gitter"}
+    ${doELFPatch "nacl_helper"}
+    ${doELFPatch "minidump_stackwalk"}
+    ${doELFPatch "nwjc"}
+    ${doELFPatch "chromedriver"}
+    ${doELFPatch "payload"}
+
+    patchelf --set-rpath "$out/${gitterDirectorySuffix}/lib:${libPath}" \
+         $out/${gitterDirectorySuffix}/lib/libnw.so
+
+    wrapProgram $out/${gitterDirectorySuffix}/Gitter --prefix LD_LIBRARY_PATH : ${libPath}
+
+    ln -s $out/${gitterDirectorySuffix}/Gitter $out/bin/
+    ln -s $out/${gitterDirectorySuffix}/logo.png $out/share/pixmaps/gitter.png
+    ln -s "${desktopItem}/share/applications" $out/share/
+  '';
+
+  desktopItem = makeDesktopItem {
+    name = pname;
+    exec = "Gitter";
+    icon = pname;
+    desktopName = "Gitter";
+    genericName = meta.description;
+    categories = "Network;InstantMessaging;";
+  };
+
+  meta = with stdenv.lib; {
+    description = "Where developers come to talk";
+    downloadPage = "https://gitter.im/apps";
+    license = licenses.mit;
+    maintainers = [ maintainers.imalison ];
+    platforms = [ "x86_64-linux" ];
+  };
+}
--- a/pkgs/applications/office/tryton/default.nix
+++ b/pkgs/applications/office/tryton/default.nix
@ -14,10 +14,10 @@ with stdenv.lib;

 python2Packages.buildPythonApplication rec {
  pname = "tryton";
-  version = "4.8.2";
+  version = "4.8.3";
  src = python2Packages.fetchPypi {
    inherit pname version;
-    sha256 = "02jnqxwsqk7hn52hc4jd59nd94d810i4psaa3lqqig3br5blp8yx";
+    sha256 = "1e2862bbe7c943afbbdf2232cdc55f75d2357640115c7f1483f0814b2c5a6882";
  };
  nativeBuildInputs = [ pkgconfig gobjectIntrospection ];
  propagatedBuildInputs = with python2Packages; [
--- a/pkgs/applications/office/trytond/default.nix
+++ b/pkgs/applications/office/trytond/default.nix
@ -5,10 +5,10 @@ with stdenv.lib;

 python2Packages.buildPythonApplication rec {
  pname = "trytond";
-  version = "4.8.1";
+  version = "4.8.2";
  src = python2Packages.fetchPypi {
    inherit pname version;
-    sha256 = "8e72a24bdf2fd090c5e12ce5f73a00322e31519608b31db44d7bb76382078db9";
+    sha256 = "ec5c419418517bf9f7d2af08b2bfd3bcc7526f6d6f07d122abf1699c728ae2a9";
  };

  # Tells the tests which database to use
--- a/pkgs/applications/science/biology/somatic-sniper/default.nix
+++ b/pkgs/applications/science/biology/somatic-sniper/default.nix
@ -0,0 +1,26 @@
+{stdenv, fetchFromGitHub, cmake, zlib, ncurses}:
+
+stdenv.mkDerivation rec {
+  name = "somatic-sniper-${version}";
+  version = "1.0.5.0";
+
+  src = fetchFromGitHub {
+    owner = "genome";
+    repo = "somatic-sniper";
+    rev = "v${version}";
+    sha256 = "0lk7p9sp6mp50f6w1nppqhr40fcwy1asw06ivw8w8jvvnwaqf987";
+  };
+
+  patches = [ ./somatic-sniper.patch ];
+
+  buildInputs = [ cmake zlib ncurses ];
+
+  meta = with stdenv.lib; {
+    description = "Identify single nucleotide positions that are different between tumor and normal";
+    license = licenses.mit;
+    homepage = https://github.com/genome/somatic-sniper;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.linux;
+  };
+
+}
--- a/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch
+++ b/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch
@ -0,0 +1,26 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 6d5a180..7254292 100644
+--- a/CMakeLists.txt
+++ b/CMakeLists.txt
+@@ -11,7 +11,7 @@ set(CMAKE_MODULE_PATH
+     )
+ 
+ include(TestHelper)
+-include(VersionHelper)
+#include(VersionHelper)
+ include(ProjectHelper)
+ 
+ # NOTE: for sniper we want the exe suffix to be like 0.7.4, not just 0.7
+diff --git a/vendor/samtools.patch b/vendor/samtools.patch
+index f173017..654f878 100644
+--- a/vendor/samtools.patch
+++ b/vendor/samtools.patch
+@@ -6,7 +6,7 @@ diff -Nuar a/Makefile b/Makefile
+  
+  samtools:lib $(AOBJS)
+ -		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
+-+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -L. -lbam -lz
++		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lncurses -L. -lbam -lz
+  
+  razip:razip.o razf.o
+  		$(CC) $(CFLAGS) -o $@ razf.o razip.o -lz
--- a/pkgs/applications/science/chemistry/openmolcas/default.nix
+++ b/pkgs/applications/science/chemistry/openmolcas/default.nix
@ -0,0 +1,72 @@
+{ stdenv, pkgs, fetchFromGitLab, cmake, gfortran, perl
+, openblas, hdf5-cpp, python3, texlive
+, armadillo, openmpi, globalarrays, openssh
+, makeWrapper
+} :
+
+let
+  version = "20180529";
+  gitLabRev = "b6b9ceffccae0dd7f14c099468334fee0b1071fc";
+
+  python = python3.withPackages (ps : with ps; [ six pyparsing ]);
+
+in stdenv.mkDerivation {
+  name = "openmolcas-${version}";
+
+  src = fetchFromGitLab {
+    owner = "Molcas";
+    repo = "OpenMolcas";
+    rev = gitLabRev;
+    sha256 = "1wbjjdv07lg1x4kdnf28anyrjgy33gdgrd5d7zi1c97nz7vhdjaz";
+  };
+
+  nativeBuildInputs = [ perl cmake texlive.combined.scheme-minimal makeWrapper ];
+  buildInputs = [
+    gfortran
+    openblas
+    hdf5-cpp
+    python
+    armadillo
+    openmpi
+    globalarrays
+    openssh
+  ];
+
+  enableParallelBuilding = true;
+
+  cmakeFlags = [
+    "-DOPENMP=ON"
+    "-DGA=ON"
+    "-DMPI=ON"
+    "-DLINALG=OpenBLAS"
+    "-DTOOLS=ON"
+    "-DHDF5=ON"
+    "-DFDE=ON"
+    "-DOPENBLASROOT=${openblas}"
+  ];
+
+  GAROOT=globalarrays;
+
+  postConfigure = ''
+    # The Makefile will install pymolcas during the build grrr.
+    mkdir -p $out/bin
+    export PATH=$PATH:$out/bin
+  '';
+
+  postFixup = ''
+    # Wrong store path in shebang (no Python pkgs), force re-patching
+    sed -i "1s:/.*:/usr/bin/env python:" $out/bin/pymolcas
+    patchShebangs $out/bin
+
+    wrapProgram $out/bin/pymolcas --set MOLCAS $out
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Advanced quantum chemistry software package";
+    homepage = https://gitlab.com/Molcas/OpenMolcas;
+    maintainers = [ maintainers.markuskowa ];
+    license = licenses.lgpl21;
+    platforms = platforms.linux;
+  };
+}
+
--- a/pkgs/applications/version-management/monotone/default.nix
+++ b/pkgs/applications/version-management/monotone/default.nix
@ -18,7 +18,7 @@ stdenv.mkDerivation rec {
    sha256 = "124cwgi2q86hagslbk5idxbs9j896rfjzryhr6z63r6l485gcp7r";
  };

-  patches = [ ];
+  patches = [ ./monotone-1.1-Adapt-to-changes-in-pcre-8.42.patch ];

  nativeBuildInputs = [ pkgconfig ];
  buildInputs = [ boost zlib botan libidn lua pcre sqlite expect 
--- a/pkgs/applications/version-management/monotone/monotone-1.1-Adapt-to-changes-in-pcre-8.42.patch
+++ b/pkgs/applications/version-management/monotone/monotone-1.1-Adapt-to-changes-in-pcre-8.42.patch
@ -0,0 +1,66 @@
+From 70f209ad582121750d54e3692b1e62c7f36af6f9 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Petr=20P=C3=ADsa=C5=99?= <ppisar@redhat.com>
+Date: Mon, 7 May 2018 14:09:06 +0200
+Subject: [PATCH] Adapt to changes in pcre-8.42
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+pcre-8.42 replaced internal real_pcre with real_pcre8_or_16. This
+broke monotone that decided not to use the public "pcre" type.
+
+This patch adapts monotone to the pcre >= 8.42.
+
+Signed-off-by: Petr Písař <ppisar@redhat.com>
+---
+ src/pcrewrap.cc | 4 ++--
+ src/pcrewrap.hh | 4 ++--
+ 2 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/src/pcrewrap.cc b/src/pcrewrap.cc
+index 8c0c9d1..30bafff 100644
+--- a/src/pcrewrap.cc
+++ b/src/pcrewrap.cc
+@@ -74,7 +74,7 @@ get_capturecount(void const * bd)
+ namespace pcre
+ {
+   typedef map<char const *,
+-              pair<struct real_pcre const *, struct pcre_extra const *> >
+              pair<struct real_pcre8_or_16 const *, struct pcre_extra const *> >
+               regex_cache;
+ 
+   class regex_cache_manager
+@@ -86,7 +86,7 @@ public:
+       }
+ 
+     void store(char const * pattern,
+-               pair<struct real_pcre const *, struct pcre_extra const *>
+               pair<struct real_pcre8_or_16 const *, struct pcre_extra const *>
+                data)
+       {
+         cache[pattern] = data;
+diff --git a/src/pcrewrap.hh b/src/pcrewrap.hh
+index 3359cdd..5008e88 100644
+--- a/src/pcrewrap.hh
+++ b/src/pcrewrap.hh
+@@ -18,7 +18,7 @@
+ // definitions and so we don't actually expose it here. Unfortunately, this
+ // means we have to hope this pair of forward declarations will not change...
+ 
+-struct real_pcre;
+struct real_pcre8_or_16;
+ struct pcre_extra;
+ 
+ namespace pcre
+@@ -61,7 +61,7 @@ namespace pcre
+     regex & operator=(regex const &);
+ 
+     // data
+-    struct real_pcre const * basedat;
+    struct real_pcre8_or_16 const * basedat;
+     struct pcre_extra const * extradat;
+ 
+     // used by constructors
+-- 
+2.14.3
+
--- a/pkgs/applications/version-management/reposurgeon/default.nix
+++ b/pkgs/applications/version-management/reposurgeon/default.nix
@ -1,17 +1,17 @@
 { stdenv, fetchurl, makeWrapper, python27Packages, git
-, docbook_xml_dtd_412, docbook_xsl, asciidoc, xmlto
+, docbook_xml_dtd_412, docbook_xsl, asciidoc, xmlto, pypy
 , bazaar ? null, cvs ? null, darcs ? null, fossil ? null
 , mercurial ? null, monotone ? null, rcs ? null
 , subversion ? null, cvs_fast_export ? null }:

 with stdenv; with lib;
 let
-  inherit (python27Packages) python cython;
+  inherit (python27Packages) python;
 in mkDerivation rec {
  name = "reposurgeon-${meta.version}";
  meta = {
    description = "A tool for editing version-control repository history";
-    version = "3.28";
+    version = "3.44";
    license = licenses.bsd3;
    homepage = http://www.catb.org/esr/reposurgeon/;
    maintainers = with maintainers; [ dfoxfranke ];
@ -19,17 +19,15 @@ in mkDerivation rec {
  };

  src = fetchurl {
-    url = "http://www.catb.org/~esr/reposurgeon/reposurgeon-3.28.tar.gz";
-    sha256 = "3225b44109b8630310a0ea6fe63a3485d27aa46deaf80e8d07820e01a6f62626";
+    url = "http://www.catb.org/~esr/reposurgeon/reposurgeon-3.44.tar.xz";
+    sha256 = "0il6hwrsm2qgg0vp5fcjh478y2x4zyw3mx2apcwc7svfj86pf7pn";
  };

-  # See https://gitlab.com/esr/reposurgeon/issues/17
-  patches = [ ./fix-preserve-type.patch ];
+  # install fails because the files README.md, NEWS, and TODO were not included in the source distribution
+  patches = [ ./fix-makefile.patch ];

  buildInputs =
-    [ docbook_xml_dtd_412 docbook_xsl asciidoc xmlto makeWrapper ] ++
-    optional (cython != null) cython
-  ;
+    [ docbook_xml_dtd_412 docbook_xsl asciidoc xmlto makeWrapper pypy ];

  preBuild = ''
    makeFlagsArray=(
@ -40,12 +38,6 @@ in mkDerivation rec {
    )
  '';

-  buildFlags = "all" + (if cython != null then " cyreposurgeon" else "");
-
-  installTargets =
-    "install" + (if cython != null then " install-cyreposurgeon" else "")
-  ;
-
  postInstall =
    let
      binpath = makeBinPath (
--- a/pkgs/applications/version-management/reposurgeon/fix-makefile.patch
+++ b/pkgs/applications/version-management/reposurgeon/fix-makefile.patch
@ -0,0 +1,12 @@
+diff -Naur reposurgeon-3.44/Makefile reposurgeon-3.44-new/Makefile
+--- reposurgeon-3.44/Makefile	2018-04-29 12:27:43.000000000 -0700
+++ reposurgeon-3.44-new/Makefile	2018-08-01 17:38:15.582789739 -0700
+@@ -36,7 +36,7 @@
+ MANPAGES = reposurgeon.1 repotool.1 repodiffer.1 repomapper.1 repocutter.1
+ HTMLFILES = $(MANPAGES:.1=.html) \
+             dvcs-migration-guide.html features.html reporting-bugs.html
+-SHARED    = README.md NEWS TODO reposurgeon-git-aliases $(HTMLFILES)
+SHARED    = reposurgeon-git-aliases $(HTMLFILES)
+ 
+ all:  $(MANPAGES) $(HTMLFILES)
+ 
--- a/pkgs/applications/version-management/reposurgeon/fix-preserve-type.patch
+++ b/pkgs/applications/version-management/reposurgeon/fix-preserve-type.patch
@ -1,12 +0,0 @@
-diff -Nru reposurgeon-3.28/reposurgeon reposurgeon-3.28-new/reposurgeon
--- reposurgeon-3.28/reposurgeon	2015-07-05 15:17:13.000000000 -0400
-+++ reposurgeon-3.28-new/reposurgeon	2015-08-25 18:23:11.347591137 -0400
-@@ -193,7 +193,7 @@
-         importer=b"git fast-import --quiet",
-         checkout=b"git checkout",
-         lister=b"git ls-files",
-        preserve=(b'.git/config', b'.git/hooks'),
-+        preserve=set((b'.git/config', b'.git/hooks')),
-         authormap=b".git/cvs-authors",
-         ignorename=b".gitignore",
-         dfltignores=b"",	# Has none
--- a/pkgs/desktops/xfce4-13/default.nix
+++ b/pkgs/desktops/xfce4-13/default.nix
@ -46,6 +46,10 @@ makeScope newScope (self: with self; {

  xfce4-battery-plugin = callPackage ./xfce4-battery-plugin { };

+  xfce4-cpufreq-plugin = callPackage ./xfce4-cpufreq-plugin { };
+
+  xfce4-clipman-plugin = callPackage ./xfce4-clipman-plugin { };
+
  xfce4-dev-tools = callPackage ./xfce4-dev-tools {
    mkXfceDerivation = mkXfceDerivation.override {
      xfce4-dev-tools = null;
@ -56,25 +60,36 @@ makeScope newScope (self: with self; {

  xfce4-mixer = callPackage ./xfce4-mixer { };

+  xfce4-netload-plugin = callPackage ./xfce4-netload-plugin { };
+
  xfce4-notifyd = callPackage ./xfce4-notifyd { };

  xfce4-panel = callPackage ./xfce4-panel { };

  xfce4-power-manager = callPackage ./xfce4-power-manager { };

+  xfce4-pulseaudio-plugin = callPackage ./xfce4-pulseaudio-plugin { };
+
  xfce4-screenshooter = callPackage ./xfce4-screenshooter {
    inherit (gnome3) libsoup;
  };

-  xfce4-taskmanager = callPackage ./xfce4-taskmanager { };
+  xfce4-session = callPackage ./xfce4-session { };
+  xinitrc = "${xfce4-session}/etc/xdg/xfce4/xinitrc";

  xfce4-settings = callPackage ./xfce4-settings { };

+  xfce4-taskmanager = callPackage ./xfce4-taskmanager { };
+
  xfce4-terminal = callPackage ./xfce4-terminal {
    inherit (gnome3) vte;
  };

  xfce4-volumed-pulse = callPackage ./xfce4-volumed-pulse { };

+  xfce4-whiskermenu-plugin = callPackage ./xfce4-whiskermenu-plugin { };
+
+  xfce4-xkb-plugin = callPackage ./xfce4-xkb-plugin { };
+
  xfwm4 = callPackage ./xfwm4 { };
 })
--- a/pkgs/desktops/xfce4-13/xfce4-clipman-plugin/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-clipman-plugin/default.nix
@ -0,0 +1,11 @@
+{ mkXfceDerivation, gtk3, libXtst, libxfce4ui, libxfce4util, xfce4-panel, xfconf, exo }:
+
+mkXfceDerivation rec {
+  category = "panel-plugins";
+  pname = "xfce4-clipman-plugin";
+  version = "1.4.2";
+  rev = version;
+  sha256 = "1c2h1cs7pycf1rhpirmvb0l0dfvlacb7xgm31q9rxmhihnycd2na";
+
+  buildInputs = [ exo gtk3 libXtst libxfce4ui libxfce4util xfce4-panel xfconf ];
+}
--- a/pkgs/desktops/xfce4-13/xfce4-cpufreq-plugin/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-cpufreq-plugin/default.nix
@ -0,0 +1,10 @@
+{ mkXfceDerivation, gtk3, libxfce4ui, libxfce4util, xfce4-panel, xfconf }:
+
+mkXfceDerivation rec {
+  category = "panel-plugins";
+  pname = "xfce4-cpufreq-plugin";
+  version = "1.2.0";
+  sha256 = "0zhs7b7py1njczmpnib4532fwpnd3vnpqfhss2r136cfgy72kp6g";
+
+  buildInputs = [ gtk3 libxfce4ui libxfce4util xfce4-panel xfconf ];
+}
--- a/pkgs/desktops/xfce4-13/xfce4-netload-plugin/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-netload-plugin/default.nix
@ -0,0 +1,11 @@
+{ mkXfceDerivation, gtk3, libxfce4ui, libxfce4util, xfce4-panel, xfconf }:
+
+mkXfceDerivation rec {
+  category = "panel-plugins";
+  pname = "xfce4-netload-plugin";
+  version = "1.3.1";
+  rev = "version-${version}";
+  sha256 = "0nm8advafw4jpc9p1qszyfqa56194sz51z216rdh4c6ilcrrpy1h";
+
+  buildInputs = [ gtk3 libxfce4ui libxfce4util xfce4-panel xfconf ];
+}
--- a/pkgs/desktops/xfce4-13/xfce4-panel/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-panel/default.nix
@ -1,4 +1,4 @@
-{ mkXfceDerivation, makeWrapper, exo, garcon, gtk2, gtk3, gettext, glib-networking, libxfce4ui, libxfce4util, libwnck3, xfconf }:
+{ mkXfceDerivation, makeWrapper, tzdata, exo, garcon, gtk2, gtk3, gettext, glib-networking, libxfce4ui, libxfce4util, libwnck3, xfconf }:

 mkXfceDerivation rec {
  category = "xfce";
@ -17,6 +17,9 @@ mkXfceDerivation rec {
    for f in $(find . -name \*.sh); do
      substituteInPlace $f --replace gettext ${gettext}/bin/gettext
    done
+    substituteInPlace plugins/clock/clock.c \
+       --replace "/usr/share/zoneinfo" "${tzdata}/share/zoneinfo" \
+       --replace "if (!g_file_test (filename, G_FILE_TEST_IS_SYMLINK))" ""
  '';

  configureFlags = [ "--enable-gtk3" ];
--- a/pkgs/desktops/xfce4-13/xfce4-pulseaudio-plugin/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-pulseaudio-plugin/default.nix
@ -0,0 +1,19 @@
+{ mkXfceDerivation, automakeAddFlags, dbus-glib, dbus, gtk3, libpulseaudio
+, libnotify, libxfce4ui, libxfce4util, xfce4-panel, xfconf }:
+
+mkXfceDerivation rec {
+  category = "panel-plugins";
+  pname = "xfce4-pulseaudio-plugin";
+  version = "0.4.1";
+  sha256 = "1c8krpg3l6ki00ldd9hifc4bddysdm0w3x5w43fkr31j0zrscvfp";
+
+  nativeBuildInputs = [ automakeAddFlags ];
+
+  NIX_CFLAGS_COMPILE = [ "-I${dbus-glib.dev}/include/dbus-1.0" "-I${dbus.dev}/include/dbus-1.0" ];
+
+  postPatch = ''
+    substituteInPlace configure.ac.in --replace gio-2.0 gio-unix-2.0
+  '';
+
+  buildInputs = [ gtk3 libnotify libpulseaudio libxfce4ui libxfce4util xfce4-panel xfconf ];
+}
--- a/pkgs/desktops/xfce4-13/xfce4-session/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-session/default.nix
@ -0,0 +1,27 @@
+{ mkXfceDerivation, polkit, exo, libxfce4util, libxfce4ui, xfconf, dbus-glib, dbus, iceauth, gtk3, libwnck3, xorg }:
+
+mkXfceDerivation rec {
+  category = "xfce";
+  pname = "xfce4-session";
+  version = "4.13.0";
+
+  sha256 = "0d6h1kgqq6g084jrxx4jxw98h5g0vwsxqrvk0bmapyxh2sbrg07y";
+
+  buildInputs = [ exo dbus-glib dbus gtk3 libxfce4ui libxfce4util libwnck3 xfconf polkit iceauth ];
+
+  configureFlags = [ "--with-xsession-prefix=$(out)" ];
+
+  NIX_CFLAGS_COMPILE = [ "-I${dbus-glib.dev}/include/dbus-1.0"
+                         "-I${dbus.dev}/include/dbus-1.0"
+                         "-I${dbus.lib}/lib/dbus-1.0/include"
+                       ];
+
+  postPatch = ''
+    substituteInPlace configure.ac.in --replace gio-2.0 gio-unix-2.0
+    substituteInPlace scripts/xflock4 --replace PATH=/bin:/usr/bin "PATH=\$PATH:$out/bin:${xorg.xset}/bin"
+  '';
+
+  meta =  {
+    description = "Session manager for Xfce";
+  };
+}
--- a/pkgs/desktops/xfce4-13/xfce4-whiskermenu-plugin/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-whiskermenu-plugin/default.nix
@ -0,0 +1,18 @@
+{ mkXfceDerivation, dbus-glib, gtk3, cmake, exo, garcon, libxfce4ui, libxfce4util, xfce4-panel, xfconf }:
+
+mkXfceDerivation rec {
+  category = "panel-plugins";
+  pname = "xfce4-whiskermenu-plugin";
+  version = "2.2.0";
+  rev = "v${version}";
+  sha256 = "1d35xxkdzw8pl3d5ps226mmrrjk0hqczsbvl5smh7l7jbwfambjm";
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ dbus-glib exo garcon gtk3 libxfce4ui libxfce4util xfce4-panel xfconf ];
+
+  postInstall = ''
+    substituteInPlace $out/bin/xfce4-popup-whiskermenu \
+      --replace $out/bin/xfce4-panel ${xfce4-panel.out}/bin/xfce4-panel
+  '';
+}
--- a/pkgs/desktops/xfce4-13/xfce4-xkb-plugin/default.nix
+++ b/pkgs/desktops/xfce4-13/xfce4-xkb-plugin/default.nix
@ -0,0 +1,11 @@
+{ mkXfceDerivation, gtk3, librsvg, libwnck3, libxklavier, garcon, libxfce4ui, libxfce4util, xfce4-panel, xfconf }:
+
+mkXfceDerivation rec {
+  category = "panel-plugins";
+  pname = "xfce4-xkb-plugin";
+  version = "0.8.1";
+  rev = version;
+  sha256 = "1gyky4raynp2ggdnq0g96c6646fjm679fzipcsmf1q0aymr8d5ky";
+
+  buildInputs = [ garcon gtk3 librsvg libxfce4ui libxfce4util libxklavier libwnck3 xfce4-panel xfconf ];
+}
--- a/pkgs/development/compilers/pakcs/adjust-buildsystem.patch
+++ b/pkgs/development/compilers/pakcs/adjust-buildsystem.patch
@ -1,21 +0,0 @@
-diff -Naur pakcs-1.11.4-upstream/scripts/pakcs.sh pakcs-1.11.4/scripts/pakcs.sh
--- pakcs-1.11.4-upstream/scripts/pakcs.sh	2014-10-24 05:06:07.000000000 -0430
-+++ pakcs-1.11.4/scripts/pakcs.sh	2015-01-05 16:26:15.697982791 -0430
-@@ -16,7 +16,7 @@
- # use readline wrapper rlwrap if it is installed and we have tty as stdin:
- USERLWRAP=no
- if tty -s ; then
-  RLWRAP=`which rlwrap`
-+  RLWRAP=`type -P rlwrap`
-   if [ -x "$RLWRAP" ] ; then
-     USERLWRAP=yes
-   fi
-@@ -29,7 +29,7 @@
- done
- 
- if [ $USERLWRAP = yes ] ; then
-  exec rlwrap -c -f "$PAKCSHOME/tools/rlwrap" "$REPL" ${1+"$@"}
-+  exec rlwrap -a -c -f "$PAKCSHOME/tools/rlwrap" "$REPL" ${1+"$@"}
- else
-   exec "$REPL" ${1+"$@"}
- fi
--- a/pkgs/development/compilers/pakcs/case-insensitive.patch
+++ b/pkgs/development/compilers/pakcs/case-insensitive.patch
@ -1,19 +0,0 @@
--- www/Makefile.orig	2016-10-10 21:04:36.000000000 +0300
-+++ pakcs-1.14.0/www/Makefile	2016-10-10 21:07:56.000000000 +0300
-@@ -6,7 +6,7 @@ all: submitform Registry
- submitform: SubmitForm.curry $(LIBDIR)/HtmlCgi.curry \
- 	    $(LIBDIR)/NamedSocket.curry $(LIBDIR)/CPNS.curry
- 	$(REPL) $(REPL_OPTS) :load SubmitForm :save :q
-	mv SubmitForm submitform
-+	mv SubmitForm submitform.orig && mv submitform.orig submitform
- 
- Registry: Registry.curry $(LIBDIR)/HtmlCgi.curry
- 	$(REPL) $(REPL_OPTS) :load Registry :save :q
--- currytools/erd2curry/Makefile.orig	2016-10-10 21:13:49.000000000 +0300
-+++ pakcs-1.14.0/currytools/erd2curry/Makefile	2016-10-10 21:21:14.000000000 +0300
-@@ -32,4 +32,4 @@ uninstall: clean
- erd2curry: $(DEPS)
- 	# create saved state for top-level function "main":
- 	$(REPL) $(REPL_OPTS) :load ERD2Curry :save "main \"$(CURDIR)\"" :q
-	mv ERD2Curry $@
-+	mv ERD2Curry $@.orig && mv $@.orig $@
--- a/pkgs/development/compilers/pakcs/curry-base.nix
+++ b/pkgs/development/compilers/pakcs/curry-base.nix
@ -0,0 +1,16 @@
+{ mkDerivation, base, Cabal, containers, directory, extra, filepath
+, mtl, parsec, pretty, stdenv, time, transformers
+}:
+mkDerivation {
+  pname = "curry-base";
+  version = "1.0.0";
+  src = ./.;
+  libraryHaskellDepends = [
+    base containers directory extra filepath mtl parsec pretty time
+    transformers
+  ];
+  testHaskellDepends = [ base Cabal filepath mtl ];
+  homepage = "http://curry-language.org";
+  description = "Functions for manipulating Curry programs";
+  license = stdenv.lib.licenses.bsd3;
+}
--- a/pkgs/development/compilers/pakcs/curry-frontend.nix
+++ b/pkgs/development/compilers/pakcs/curry-frontend.nix
@ -0,0 +1,24 @@
+{ mkDerivation, base, Cabal, containers, curry-base, directory
+, extra, filepath, mtl, network-uri, pretty, process, set-extra
+, stdenv, transformers
+}:
+mkDerivation {
+  pname = "curry-frontend";
+  version = "1.0.2";
+  src = ./.;
+  isLibrary = true;
+  isExecutable = true;
+  enableSeparateDataOutput = true;
+  libraryHaskellDepends = [
+    base containers curry-base directory extra filepath mtl network-uri
+    pretty process set-extra transformers
+  ];
+  executableHaskellDepends = [
+    base containers curry-base directory extra filepath mtl network-uri
+    pretty process set-extra transformers
+  ];
+  testHaskellDepends = [ base Cabal curry-base filepath ];
+  homepage = "http://curry-language.org";
+  description = "Compile the functional logic language Curry to several intermediate formats";
+  license = stdenv.lib.licenses.bsd3;
+}
--- a/pkgs/development/compilers/pakcs/default.nix
+++ b/pkgs/development/compilers/pakcs/default.nix
@ -1,139 +1,72 @@
-{ stdenv, fetchurl, swiProlog, haskellPackages
-, glibcLocales, makeWrapper, rlwrap, tk, which }:
+{ stdenv, fetchurl, makeWrapper
+, haskellPackages, haskell
+, which, swiProlog, rlwrap, tk
+, curl, git, unzip, gnutar, coreutils, sqlite }:

 let
-  fname = "pakcs-1.14.0";
+  name = "pakcs-2.0.2";

-  fsrc = fetchurl {
-    url = "https://www.informatik.uni-kiel.de/~pakcs/download/${fname}-src.tar.gz";
-    sha256 = "1651ssh4ql79x8asd7kp4yis2n5rhn3lml4s26y03b0cgbfhs78s";
+  src = fetchurl {
+    url = "https://www.informatik.uni-kiel.de/~pakcs/download/${name}-src.tar.gz";
+    sha256 = "0fdzw2zz5vs6z20jn6a8jfvpr6dp7fs1rr01cy0xjnzg2mgmn42a";
  };

-  swiPrologLocked = stdenv.lib.overrideDerivation swiProlog (oldAttrs: rec {
-    version = "6.6.6";
-    name = "swi-prolog-${version}";
-    src = fetchurl {
-      url = "http://www.swi-prolog.org/download/stable/src/pl-${version}.tar.gz";
-      sha256 = "0vcrfskm2hyhv30lxr6v261myb815jc3bgmcn1lgsc9g9qkvp04z";
+  curry-frontend = (haskellPackages.override {
+    overrides = self: super: {
+      curry-base = haskell.lib.overrideCabal (super.callPackage ./curry-base.nix {}) (drv: {
+        inherit src;
+        postUnpack = "sourceRoot+=/frontend/curry-base";
+      });
+      curry-frontend = haskell.lib.overrideCabal (super.callPackage ./curry-frontend.nix {}) (drv: {
+        inherit src;
+        postUnpack = "sourceRoot+=/frontend/curry-frontend";
+      });
    };
-  });
+  }).curry-frontend;
+in stdenv.mkDerivation {
+  inherit name src;

-in
-stdenv.mkDerivation rec {
+  buildInputs = [ swiProlog ];
+  nativeBuildInputs = [ which makeWrapper ];

-  name = fname;
-
-  curryBase = haskellPackages.callPackage (
-    { mkDerivation, base, Cabal, containers, directory, either
-    , filepath, mtl, pretty, syb, time
-    }:
-    mkDerivation {
-      pname = "curry-base";
-      version = "0.4.1";
-      src = fsrc;
-      libraryHaskellDepends = [
-        base containers directory either filepath mtl pretty syb time
-      ];
-      testHaskellDepends = [ base Cabal filepath mtl ];
-      homepage = http://curry-language.org;
-      description = "Functions for manipulating Curry programs";
-      license = "unknown";
-
-      postUnpack = ''
-        mv ${name} ${name}.orig
-        ln -s ${name}.orig/frontend/curry-base ${name}
-      '';
-      doCheck = false;
-    }
-  ) {};
-
-  curryFront = haskellPackages.callPackage (
-    { mkDerivation, base, Cabal, containers, directory
-    , filepath, mtl, network-uri, process, syb, transformers
-    }:
-    mkDerivation {
-      pname = "curry-frontend";
-      version = "0.4.1";
-      src = fsrc;
-      isLibrary = true;
-      isExecutable = true;
-      libraryHaskellDepends = [
-        base containers curryBase directory filepath mtl network-uri
-        process syb transformers
-      ];
-      executableHaskellDepends = [
-        base containers curryBase directory filepath mtl network-uri
-        process syb transformers
-      ];
-      testHaskellDepends = [ base Cabal curryBase filepath ];
-      homepage = http://curry-language.org;
-      description = "Compile the functional logic language Curry to several intermediate formats";
-      license = "unknown";
-
-      postUnpack = ''
-        mv ${name} ${name}.orig
-        ln -s ${name}.orig/frontend/curry-frontend ${name}
-      '';
-      doCheck = false;
-    }
-  ) {};
-
-  src = fsrc;
-
-  buildInputs = [ swiPrologLocked makeWrapper glibcLocales rlwrap tk which ];
-
-  patches = [
-    ./adjust-buildsystem.patch
-    ./case-insensitive.patch
+  makeFlags = [
+    "CURRYFRONTEND=${curry-frontend}/bin/curry-frontend"
+    "DISTPKGINSTALL=yes"
+    # Not needed, just to make script pass
+    "CURRYTOOLSDIR=0"
+    "CURRYLIBSDIR=0"
  ];

-  configurePhase = ''
-    # Phony HOME.
-    mkdir phony-home
-    export HOME=$(pwd)/phony-home
+  preConfigure = ''
+    # Since we can't expand $out in `makeFlags`
+    #makeFlags="$makeFlags PAKCSINSTALLDIR=$out/pakcs"

-    # SWI Prolog
-    sed -i 's@SWIPROLOG=@SWIPROLOG='${swiPrologLocked}/bin/swipl'@' scripts/pakcsinitrc.sh
+    substituteInPlace currytools/cpm/src/CPM/Repository.curry \
+      --replace "/bin/rm" "rm"
  '';

+  # cypm new: EXISTENCE ERROR: source_sink
+  # "/tmp/nix-build-pakcs-2.0.2.drv-0/pakcs-2.0.2/currytools/cpm/templates/LICENSE"
+  # does not exist
  buildPhase = ''
-    # Some comments in files are in UTF-8, so include the locale needed by GHC runtime.
-    export LC_ALL=en_US.UTF-8
-
-    # PAKCS must be build in place due to embedded filesystem references placed by swi.
-
-    # Prepare PAKCSHOME directory.
-    mkdir -p $out/pakcs/bin
-
-    # Set up link to cymake, which has been built already.
-    ln -s ${curryFront}/bin/cymake $out/pakcs/bin/
-    rm -r frontend
-
-    # Prevent embedding the derivation build directory as temp.
-    export TEMP=/tmp
-
-    # Copy to in place build location and run the build.
+    mkdir -p $out/pakcs
    cp -r * $out/pakcs
-    (cd $out/pakcs ; make)
+    (cd $out/pakcs ; make -j$NIX_BUILD_CORES $makeFlags)
  '';

  installPhase = ''
-    # Install bin.
-    mkdir -p $out/bin
-    for b in $(ls $out/pakcs/bin) ; do
-      ln -s $out/pakcs/bin/$b $out/bin/ ;
-    done
+    ln -s $out/pakcs/bin $out

-    # Place emacs lisp files in expected locations.
-    mkdir -p $out/share/emacs/site-lisp/curry-pakcs
-    for e in "$out/pakcs/tools/emacs/"*.el ; do
-      cp $e $out/share/emacs/site-lisp/curry-pakcs/ ;
-    done
+    mkdir -p $out/share/emacs/site-lisp
+    ln -s $out/pakcs/tools/emacs $out/share/emacs/site-lisp/curry-pakcs

-    # Wrap for rlwrap and tk support.
    wrapProgram $out/pakcs/bin/pakcs \
      --prefix PATH ":" "${rlwrap}/bin" \
-      --prefix PATH ":" "${tk}/bin" \
+      --prefix PATH ":" "${tk}/bin"
+
+    # List of dependencies from currytools/cpm/src/CPM/Main.curry
+    wrapProgram $out/pakcs/bin/cypm \
+      --prefix PATH ":" "${stdenv.lib.makeBinPath [ curl git unzip gnutar coreutils sqlite ]}"
  '';

  meta = with stdenv.lib; {
@ -154,6 +87,6 @@ stdenv.mkDerivation rec {
    '';

    maintainers = with maintainers; [ kkallio gnidorah ];
-    platforms = platforms.unix;
+    platforms = platforms.linux;
  };
 }
--- a/pkgs/development/haskell-modules/configuration-common.nix
+++ b/pkgs/development/haskell-modules/configuration-common.nix
@ -1125,4 +1125,7 @@ self: super: {
  # Tests require a browser: https://github.com/ku-fpg/blank-canvas/issues/73
  blank-canvas = dontCheck super.blank-canvas;
  blank-canvas_0_6_2 = dontCheck super.blank-canvas_0_6_2;
+
+  # needed because of testing-feat >=0.4.0.2 && <1.1
+  language-ecmascript = doJailbreak super.language-ecmascript;
 }
--- a/pkgs/development/idris-modules/graphviz.nix
+++ b/pkgs/development/idris-modules/graphviz.nix
@ -22,7 +22,7 @@ build-idris-package  {

  meta = {
    description = "Parser and library for graphviz dot files";
-    homepage = https://github.com/mgttlinger/idris-graphviz;
+    homepage = https://gitlab.com/mgttlinger/idris-graphviz;
    license = lib.licenses.gpl3;
    maintainers = [ lib.maintainers.brainrape ];
  };
--- a/pkgs/development/interpreters/python/cpython/3.4/default.nix
+++ b/pkgs/development/interpreters/python/cpython/3.4/default.nix
@ -27,7 +27,7 @@ with stdenv.lib;

 let
  majorVersion = "3.4";
-  minorVersion = "8";
+  minorVersion = "9";
  minorVersionSuffix = "";
  version = "${majorVersion}.${minorVersion}${minorVersionSuffix}";
  libPrefix = "python${majorVersion}";
@ -49,7 +49,7 @@ in stdenv.mkDerivation {

  src = fetchurl {
    url = "http://www.python.org/ftp/python/${version}/Python-${version}.tar.xz";
-    sha256 = "1sn3i9z9m56inlfrqs250qv8snl8w211wpig2pfjlyrcj3x75919";
+    sha256 = "1n9b1kavmw8b7rc3gkrka4fjzrbfq9iqy791yncaf09bp9v9cqjr";
  };

  NIX_LDFLAGS = optionalString stdenv.isLinux "-lgcc_s";
--- a/pkgs/development/interpreters/python/cpython/3.5/default.nix
+++ b/pkgs/development/interpreters/python/cpython/3.5/default.nix
@ -27,7 +27,7 @@ with stdenv.lib;

 let
  majorVersion = "3.5";
-  minorVersion = "5";
+  minorVersion = "6";
  minorVersionSuffix = "";
  version = "${majorVersion}.${minorVersion}${minorVersionSuffix}";
  libPrefix = "python${majorVersion}";
@ -49,7 +49,7 @@ in stdenv.mkDerivation {

  src = fetchurl {
    url = "https://www.python.org/ftp/python/${majorVersion}.${minorVersion}/Python-${version}.tar.xz";
-    sha256 = "02ahsijk3a42sdzfp2il49shx0v4birhy7kkj0dikmh20hxjqg86";
+    sha256 = "0pqmf51zy2lzhbaj4yya2py2qr653j9152d0rg3p7wi1yl2dwp7m";
  };

  NIX_LDFLAGS = optionalString stdenv.isLinux "-lgcc_s";
--- a/pkgs/development/interpreters/python/pypy/2.7/default.nix
+++ b/pkgs/development/interpreters/python/pypy/2.7/default.nix
@ -10,7 +10,7 @@
 assert zlibSupport -> zlib != null;

 let
-  majorVersion = "5.10";
+  majorVersion = "6.0";
  minorVersion = "0";
  minorVersionSuffix = "";
  pythonVersion = "2.7";
@ -26,7 +26,7 @@ in stdenv.mkDerivation rec {

  src = fetchurl {
    url = "https://bitbucket.org/pypy/pypy/get/release-pypy${pythonVersion}-v${version}.tar.bz2";
-    sha256 = "10j1s6r6iv80nvpi6gv8w05v505h2ndj9xx31yz7d50ab04dfg23";
+    sha256 = "1qjwpc8n68sxxlfg36s5vn1h2gdfvvd6lxvr4lzbvfwhzrgqahsw";
  };

  nativeBuildInputs = [ pkgconfig makeWrapper ];
--- a/pkgs/development/libraries/ffmpeg-full/default.nix
+++ b/pkgs/development/libraries/ffmpeg-full/default.nix
@ -233,11 +233,11 @@ assert nvenc -> nvidia-video-sdk != null && nonfreeLicensing;

 stdenv.mkDerivation rec {
  name = "ffmpeg-full-${version}";
-  version = "4.0.1";
+  version = "4.0.2";

  src = fetchurl {
    url = "https://www.ffmpeg.org/releases/ffmpeg-${version}.tar.xz";
-    sha256 = "1vn04n0n46zdxq14cma3w8ml2ckh5jxwlybsc4xmvcqdqq0mqpv0";
+    sha256 = "15rgzcmdccy4flajs63gkz4n3k24wkkg50r13l1r83lrxg4hqp59";
  };

  prePatch = ''
--- a/pkgs/development/libraries/ffmpeg/4.nix
+++ b/pkgs/development/libraries/ffmpeg/4.nix
@ -6,7 +6,7 @@

 callPackage ./generic.nix (args // rec {
  version = "${branch}";
-  branch = "4.0.1";
-  sha256 = "0w0nq98sn5jwx982wzg3vfrxv4p0k1fvsksiz9az0rpvwyqr3rby";
+  branch = "4.0.2";
+  sha256 = "0mnh41j3kzi3x3clai1yhqasr1kc8zvd5cz0283pxhs2bxrm2v1l";
  darwinFrameworks = [ Cocoa CoreMedia ];
 })
--- a/pkgs/development/libraries/globalarrays/default.nix
+++ b/pkgs/development/libraries/globalarrays/default.nix
@ -0,0 +1,42 @@
+{ stdenv, pkgs, fetchFromGitHub, automake, autoconf, libtool
+, openblas, gfortran, openssh, openmpi
+} :
+
+let
+  version = "5.7";
+
+in stdenv.mkDerivation {
+  name = "globalarrays-${version}";
+
+  src = fetchFromGitHub {
+    owner = "GlobalArrays";
+    repo = "ga";
+    rev = "v${version}";
+    sha256 = "07i2idaas7pq3in5mdqq5ndvxln5q87nyfgk3vzw85r72c4fq5jh";
+  };
+
+  nativeBuildInputs = [ automake autoconf libtool ];
+  buildInputs = [ openmpi openblas gfortran openssh ];
+
+  preConfigure = ''
+    autoreconf -ivf
+    configureFlagsArray+=( "--enable-i8" \
+                           "--with-mpi" \
+                           "--with-mpi3" \
+                           "--enable-eispack" \
+                           "--enable-underscoring" \
+                           "--with-blas8=${openblas}/lib -lopenblas" )
+  '';
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    description = "Global Arrays Programming Models";
+    homepage = http://hpc.pnl.gov/globalarrays/;
+    maintainers = [ maintainers.markuskowa ];
+    license = licenses.bsd3;
+    platforms = platforms.linux;
+  };
+}
+
+
--- a/pkgs/development/libraries/libtorrent-rasterbar/default.nix
+++ b/pkgs/development/libraries/libtorrent-rasterbar/default.nix
@ -2,7 +2,7 @@
 , boost, openssl, libtool, python, libiconv, geoip }:

 let
-  version = "1.1.7";
+  version = "1.1.9";
  formattedVersion = lib.replaceChars ["."] ["_"] version;

  boostPython = boost.override { enablePython = true; };
@ -14,20 +14,9 @@ in stdenv.mkDerivation {
    owner = "arvidn";
    repo = "libtorrent";
    rev = "libtorrent-${formattedVersion}";
-    sha256 = "073nb7yca5jg1i8z5h76qrmddl2hdy8fc1pnchkg574087an31r3";
+    sha256 = "04w3pjzd6q9wplj1dcphylxn1i2b2x0iw1l0ma58ymh14swdah7a";
  };

-  patches = [
-    (fetchpatch {
-      url = "https://github.com/arvidn/libtorrent/commit/64d6b4900448097b0157abb328621dd211e2947d.patch";
-      sha256 = "1bdv0icqzbg1il60sckcly4y22lkdbkkwdjadwdzxv7cdj586bzd";
-    })
-    (fetchpatch {
-      url = "https://github.com/arvidn/libtorrent/commit/9cd0ae67e74a507c1b9ff9c057ee97dda38ccb81.patch";
-      sha256 = "1cscqpc6fq9iwspww930dsxf0yb01bgrghzf5hdhl09a87r6q2zg";
-    })
-  ];
-
  enableParallelBuilding = true;
  nativeBuildInputs = [ automake autoconf libtool pkgconfig ];
  buildInputs = [ boostPython openssl zlib python libiconv geoip ];
--- a/pkgs/development/libraries/opencollada/default.nix
+++ b/pkgs/development/libraries/opencollada/default.nix
@ -31,5 +31,6 @@ stdenv.mkDerivation rec {
    homepage = https://github.com/KhronosGroup/OpenCOLLADA/;
    maintainers = [ stdenv.lib.maintainers.eelco ];
    platforms = stdenv.lib.platforms.unix;
+    license = stdenv.lib.licenses.mit;
  };
 }
--- a/pkgs/development/libraries/pybind11/default.nix
+++ b/pkgs/development/libraries/pybind11/default.nix
@ -0,0 +1,35 @@
+{ stdenv, fetchFromGitHub, cmake, python }:
+
+stdenv.mkDerivation rec {
+  name = "pybind-${version}";
+  version = "2.2.2";
+  src = fetchFromGitHub {
+    owner = "pybind";
+    repo = "pybind11";
+    rev = "v${version}";
+    sha256 = "0x71i1n5d02hjbdcnkscrwxs9pb8kplmdpqddhsimabfp84fip48";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  # disable tests as some tests (test_embed/test_interpreter) are failing at the moment
+  cmakeFlags = [
+     "-DPYTHON_EXECUTABLE=${python.interpreter}"
+     "-DPYBIND11_TEST=0"
+  ];
+  doCheck = false;
+
+  meta = {
+    homepage = https://github.com/pybind/pybind11;
+    description = "Seamless operability between C++11 and Python";
+    longDescription = ''
+      Pybind11 is a lightweight header-only library that exposes
+      C++ types in Python and vice versa, mainly to create Python
+      bindings of existing C++ code.
+    '';
+    platforms = with stdenv.lib.platforms; unix;
+    license = stdenv.lib.licenses.bsd3;
+    maintainers = with stdenv.lib.maintainers; [ yuriaisaka ];
+  };
+
+}
--- a/pkgs/development/libraries/unixODBCDrivers/default.nix
+++ b/pkgs/development/libraries/unixODBCDrivers/default.nix
@ -1,4 +1,4 @@
-{ fetchurl, stdenv, unixODBC, cmake, postgresql, mysql55, mariadb, sqlite, zlib, libxml2 }:
+{ fetchurl, stdenv, unixODBC, cmake, postgresql, mysql55, mariadb, sqlite, zlib, libxml2, dpkg, lib, openssl, kerberos, curl, libuuid, autoPatchelfHook }:

 # I haven't done any parameter tweaking.. So the defaults provided here might be bad

@ -119,4 +119,45 @@
      maintainers = with maintainers; [ vlstill ];
    };
  };
+
+  msodbcsql17 = stdenv.mkDerivation rec {
+    name = "msodbcsql17-${version}";
+    version = "${versionMajor}.${versionMinor}.${versionAdditional}-1";
+
+    versionMajor = "17";
+    versionMinor = "2";
+    versionAdditional = "0.1";
+
+    src = fetchurl {
+      url = "https://packages.microsoft.com/debian/9/prod/pool/main/m/msodbcsql17/msodbcsql${versionMajor}_${version}_amd64.deb";
+      sha256 = "1966ymbbk0jsacqwzi3dmhxv2n8hfgnpjsx3hr3n7s9d88chgpx5";
+    };
+
+    nativeBuildInputs = [ autoPatchelfHook ];
+    buildInputs = [ unixODBC dpkg openssl kerberos curl libuuid stdenv.cc.cc ];
+
+    unpackPhase = "dpkg -x $src ./";
+    buildPhase = "";
+
+    installPhase = ''
+      mkdir -p $out
+      mkdir -p $out/lib
+      ln -s ${lib.getLib openssl}/lib/libssl.so.1.0.0 $out/lib/libssl.so.1.0.2
+      ln -s ${lib.getLib openssl}/lib/libcrypto.so.1.0.0 $out/lib/libcrypto.so.1.0.2
+      cp -r opt/microsoft/msodbcsql${versionMajor}/lib64 opt/microsoft/msodbcsql${versionMajor}/share $out/
+    '';
+
+    passthru = {
+      fancyName = "ODBC Driver 17 for SQL Server";
+      driver = "lib/libmsodbcsql-${versionMajor}.${versionMinor}.so.${versionAdditional}";
+    };
+
+    meta = with stdenv.lib; {
+      description = "ODBC Driver 17 for SQL Server";
+      homepage = https://docs.microsoft.com/en-us/sql/connect/odbc/linux-mac/installing-the-microsoft-odbc-driver-for-sql-server?view=sql-server-2017;
+      license = licenses.unfree;
+      platforms = platforms.linux;
+      maintainers = with maintainers; [ spencerjanssen ];
+    };
+  };
 }
--- a/pkgs/development/python-modules/carbon/default.nix
+++ b/pkgs/development/python-modules/carbon/default.nix
@ -0,0 +1,24 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, twisted, whisper, txamqp, cachetools, urllib3
+}:
+
+buildPythonPackage rec {
+  pname = "carbon";
+  version = "1.1.3";
+
+  disabled = isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1s7327p30w4l9ak4gc7m5ga521233179n2lr3j0ggfbmfhd6blky";
+  };
+
+  propagatedBuildInputs = [ twisted whisper txamqp cachetools urllib3 ];
+
+  meta = with stdenv.lib; {
+    homepage = http://graphite.wikidot.com/;
+    description = "Backend data caching and persistence daemon for Graphite";
+    maintainers = with maintainers; [ rickynils offline basvandijk ];
+    license = licenses.asl20;
+  };
+}
--- a/pkgs/development/python-modules/graphite-web/default.nix
+++ b/pkgs/development/python-modules/graphite-web/default.nix
@ -0,0 +1,54 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k, which
+, django, django_tagging, whisper, pycairo, cairocffi, ldap, memcached, pytz, urllib3, scandir
+}:
+if django.version != "1.8.18"
+|| django_tagging.version != "0.4.3"
+then throw "graphite-web should be build with django_1_8 and django_tagging_0_4_3"
+else buildPythonPackage rec {
+  pname = "graphite-web";
+  version = "1.1.3";
+
+  disabled = isPy3k;
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0nvyq1859abdch2l90avsjk9vb03s7wgxgrjsqvjhf2b9c1ncsfh";
+  };
+
+  propagatedBuildInputs = [
+    django django_tagging whisper pycairo cairocffi
+    ldap memcached pytz urllib3 scandir
+  ];
+
+  postInstall = ''
+    wrapProgram $out/bin/run-graphite-devel-server.py \
+      --prefix PATH : ${which}/bin
+  '';
+
+  preConfigure = ''
+    # graphite is configured by storing a local_settings.py file inside the
+    # graphite python package. Since that package is stored in the immutable
+    # Nix store we can't modify it. So how do we configure graphite?
+    #
+    # First of all we rename "graphite.local_settings" to
+    # "graphite_local_settings" so that the settings are not looked up in the
+    # graphite package anymore. Secondly we place a directory containing a
+    # graphite_local_settings.py on the PYTHONPATH in the graphite module
+    # <nixpkgs/nixos/modules/services/monitoring/graphite.nix>.
+    substituteInPlace webapp/graphite/settings.py \
+      --replace "graphite.local_settings" " graphite_local_settings"
+
+    substituteInPlace webapp/graphite/settings.py \
+      --replace "join(WEBAPP_DIR, 'content')" "join('$out', 'webapp', 'content')"
+  '';
+
+  # error: invalid command 'test'
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    homepage = http://graphite.wikidot.com/;
+    description = "Enterprise scalable realtime graphing";
+    maintainers = with maintainers; [ rickynils offline basvandijk ];
+    license = licenses.asl20;
+  };
+}
--- a/pkgs/development/python-modules/graphite_beacon/default.nix
+++ b/pkgs/development/python-modules/graphite_beacon/default.nix
@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, tornado, pyyaml, funcparserlib
+}:
+buildPythonPackage rec {
+  pname = "graphite_beacon";
+  version = "0.27.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "03bp4wyfn3xhcqyvs5hnk1n87m4smsmm1p7qp459m7j8hwpbq2ks";
+  };
+
+  propagatedBuildInputs = [ tornado pyyaml funcparserlib ];
+
+  postPatch = ''
+    substituteInPlace requirements.txt --replace "==" ">="
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A simple alerting application for Graphite metrics";
+    homepage = https://github.com/klen/graphite-beacon;
+    maintainers = [ maintainers.offline ];
+    license = licenses.mit;
+  };
+}
--- a/pkgs/development/python-modules/graphitepager/default.nix
+++ b/pkgs/development/python-modules/graphitepager/default.nix
@ -0,0 +1,32 @@
+{ stdenv, buildPythonPackage, fetchPypi
+, jinja2, markupsafe, pagerduty, pushbullet, python_magic, python-simple-hipchat
+, pyyaml, redis, requests, six, websocket_client, nose
+}:
+buildPythonPackage rec {
+  pname = "graphitepager";
+  version = "0.2.11";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0v3g1qcgnkpgjzh6phnv13lnk8qjrcs9sq2qg6k0dk5ik31jfk3d";
+  };
+
+  propagatedBuildInputs = [
+    jinja2 markupsafe pagerduty pushbullet python_magic python-simple-hipchat
+    pyyaml redis requests six websocket_client
+  ];
+
+  postPatch = ''
+    substituteInPlace requirements.txt --replace "==" ">="
+  '';
+
+  checkInputs = [ nose ];
+  checkPhase = "nosetests";
+
+  meta = with stdenv.lib; {
+    description = "A simple alerting application for Graphite metrics";
+    homepage = https://github.com/seatgeek/graphite-pager;
+    maintainers = with maintainers; [ offline basvandijk ];
+    license = licenses.bsd2;
+  };
+}
--- a/pkgs/development/python-modules/influxgraph/default.nix
+++ b/pkgs/development/python-modules/influxgraph/default.nix
@ -0,0 +1,30 @@
+{ stdenv, buildPythonPackage, fetchPypi, isPy3k
+, influxdb, graphite_api, memcached, gnugrep
+}:
+
+buildPythonPackage rec {
+  pname = "influxgraph";
+  version = "1.5.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0l33sfwdh4bfprmzp2kx0d9098g6yxbnhyyx9qr3kzczpm0jg9vy";
+  };
+
+  patchPhase = stdenv.lib.optionalString isPy3k ''
+    sed 's/python-memcached/python3-memcached/' \
+      -i ./influxgraph.egg-info/requires.txt    \
+      -i ./setup.py
+  '';
+
+  propagatedBuildInputs = [ influxdb graphite_api memcached ];
+
+  passthru.moduleName = "influxgraph.InfluxDBFinder";
+
+  meta = with stdenv.lib; {
+    description = "InfluxDB storage plugin for Graphite-API";
+    homepage = https://github.com/InfluxGraph/influxgraph;
+    license = licenses.asl20;
+    maintainers = with maintainers; [ basvandijk ];
+  };
+}
--- a/pkgs/development/python-modules/palettable/default.nix
+++ b/pkgs/development/python-modules/palettable/default.nix
@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi, pytest }:
+
+buildPythonPackage rec {
+  pname = "palettable";
+  version = "3.1.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0685b223a236bb7e2a900ef7a855ccf9a4027361c8acf400f3b350ea51870f80";
+  };
+
+  checkInputs = [ pytest ];
+ 
+  checkPhase = ''
+    pytest 
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A library of color palettes";
+    homepage = https://jiffyclub.github.io/palettable/;
+    license = licenses.mit;
+    maintainers = with maintainers; [ psyanticy ];
+  };
+}
+
--- a/pkgs/development/python-modules/phonopy/default.nix
+++ b/pkgs/development/python-modules/phonopy/default.nix
@ -0,0 +1,27 @@
+{ stdenv, buildPythonPackage, python, fetchPypi, numpy, pyyaml, matplotlib, h5py }:
+
+buildPythonPackage rec {
+  pname = "phonopy";
+  version = "1.13.2.13";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "23970ecdf698e743f9204711e8edfbb33c97667f5f88c7bda3322abbc91d0682";
+  };
+
+  propagatedBuildInputs = [ numpy pyyaml matplotlib h5py ];
+  
+  checkPhase = ''
+    cd test/phonopy
+    ${python.interpreter} -m unittest discover -b
+    cd ../..
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A package for phonon calculations at harmonic and quasi-harmonic levels";
+    homepage = https://atztogo.github.io/phonopy/;
+    license = licenses.bsd0;
+    maintainers = with maintainers; [ psyanticy ];
+  };
+}
+
--- a/pkgs/development/python-modules/pymatgen/default.nix
+++ b/pkgs/development/python-modules/pymatgen/default.nix
@ -0,0 +1,25 @@
+{ stdenv, buildPythonPackage, fetchPypi, glibcLocales, numpy, pydispatcher, sympy, requests, monty, ruamel_yaml, six, scipy, tabulate, enum34, matplotlib, palettable, spglib, pandas }:
+
+buildPythonPackage rec {
+  pname = "pymatgen";
+  version = "2018.6.27";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "8078af7fda4f9a07f1e389ffe08de3511213acdf9fb2ed9f9ffe89b9b12b8568";
+  };
+
+  nativeBuildInputs = [ glibcLocales ];
+  propagatedBuildInputs = [ numpy pydispatcher sympy requests monty ruamel_yaml six scipy tabulate enum34 matplotlib palettable spglib pandas ];
+  
+  # No tests in pypi tarball.
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "A robust materials analysis code that defines core object representations for structures and molecules";
+    homepage = http://pymatgen.org/;
+    license = licenses.mit;
+    maintainers = with maintainers; [ psyanticy ];
+  };
+}
+
--- a/pkgs/development/python-modules/spglib/default.nix
+++ b/pkgs/development/python-modules/spglib/default.nix
@ -2,11 +2,11 @@

 buildPythonPackage rec {
  pname = "spglib";
-  version = "1.10.3.75";
+  version = "1.10.4.1";

  src = fetchPypi {
    inherit pname version;
-    sha256 = "347fea7c87f7d2162fabb780560665d21a43cbd7a0af08328130ba26e6422143";
+    sha256 = "1a50c48dfea450c431a6d6790aa2ebbb10dc43eef97f2794f5038ed1eeecbd30";
  };

  propagatedBuildInputs = [ numpy ];
@ -22,6 +22,5 @@ buildPythonPackage rec {
    license = licenses.bsd3;
    maintainers = with maintainers; [ psyanticy ];
  };
-
 }

--- a/pkgs/development/python-modules/sumo/default.nix
+++ b/pkgs/development/python-modules/sumo/default.nix
@ -0,0 +1,24 @@
+{ stdenv, buildPythonPackage, fetchFromGitHub, numpy, scipy, spglib, pymatgen, h5py, matplotlib, seekpath, phonopy }:
+
+buildPythonPackage rec {
+  pname = "sumo";
+  version = "1.0.9";
+
+  # No tests in Pypi tarball
+  src = fetchFromGitHub {
+    owner = "SMTG-UCL";
+    repo = "sumo";
+    rev = "v${version}";
+    sha256 = "1zw86qp9ycw2k0anw6pzvwgd3zds0z2cwy0s663zhiv9mnb5hx1n";
+  };
+
+  propagatedBuildInputs = [ numpy scipy spglib pymatgen h5py matplotlib seekpath phonopy ];
+  
+  meta = with stdenv.lib; {
+    description = "Toolkit for plotting and analysis of ab initio solid-state calculation data";
+    homepage = https://github.com/SMTG-UCL/sumo;
+    license = licenses.mit;
+    maintainers = with maintainers; [ psyanticy ];
+  };
+}
+
--- a/pkgs/development/python-modules/whisper/default.nix
+++ b/pkgs/development/python-modules/whisper/default.nix
@ -0,0 +1,20 @@
+{ stdenv, buildPythonPackage, fetchPypi, six }:
+
+buildPythonPackage rec {
+  pname = "whisper";
+  version = "1.1.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ahzsxk52ws8k3kdq52qbsbsx2r9z350j8gg9adw4x5fjwksz4r8";
+  };
+
+  propagatedBuildInputs = [ six ];
+
+  meta = with stdenv.lib; {
+    homepage = http://graphite.wikidot.com/;
+    description = "Fixed size round-robin style database";
+    maintainers = with maintainers; [ rickynils offline basvandijk ];
+    license = licenses.asl20;
+  };
+}
--- a/pkgs/development/tools/icestorm/default.nix
+++ b/pkgs/development/tools/icestorm/default.nix
@ -2,13 +2,13 @@

 stdenv.mkDerivation rec {
  name = "icestorm-${version}";
-  version = "2018.05.03";
+  version = "2018.08.01";

  src = fetchFromGitHub {
    owner  = "cliffordwolf";
    repo   = "icestorm";
-    rev    = "237280ce44f72c7b2e1ca671d5113dba34cc4fca";
-    sha256 = "0r9xh024snaf1g2r5k524yl6lvf5rkfhqwjzcixh1m12012i5hrh";
+    rev    = "8cac6c584044034210fe0ba1e6b930ff1cc59465";
+    sha256 = "01cnmk4khbbgzc308qj04sfwg0r8b9nh3s7xjsxdjcb3h1m9w88c";
  };

  nativeBuildInputs = [ pkgconfig ];
--- a/pkgs/development/tools/jq/darwin-strptime-test.patch
+++ b/pkgs/development/tools/jq/darwin-strptime-test.patch
@ -0,0 +1,16 @@
+diff --git a/tests/jq.test b/tests/jq.test
+index 4a4018b..f5aa7d5 100644
+--- a/src/tests/jq.test
+++ b/src/tests/jq.test
+@@ -1144,9 +1144,9 @@ bsearch(4)
+ [1,2,3]
+ -4
+ 
+-[strptime("%Y-%m-%dT%H:%M:%SZ")|(.,mktime)]
+[strptime("%Y-%m-%dT%H:%M:%SZ")|mktime]
+ "2015-03-05T23:51:47Z"
+-[[2015,2,5,23,51,47,4,63],1425599507]
+[1425599507]
+ 
+ strftime("%Y-%m-%dT%H:%M:%SZ")
+ [2015,2,5,23,51,47,4,63]
--- a/pkgs/development/tools/jq/default.nix
+++ b/pkgs/development/tools/jq/default.nix
@ -24,7 +24,9 @@ stdenv.mkDerivation rec {
      url = https://patch-diff.githubusercontent.com/raw/stedolan/jq/pull/1214.diff;
      sha256 = "1w8bapnyp56di6p9casbfczfn8258rw0z16grydavdjddfm280l9";
    })
-  ];
+  ]
+    ++ stdenv.lib.optional stdenv.isDarwin ./darwin-strptime-test.patch;
+
  patchFlags = [ "-p2" ]; # `src` subdir was introduced after v1.5 was released

  configureFlags =
--- a/pkgs/development/tools/misc/pwndbg/default.nix
+++ b/pkgs/development/tools/misc/pwndbg/default.nix
@ -1,13 +1,14 @@
 { stdenv, fetchFromGitHub, pythonPackages, makeWrapper, gdb }:

 stdenv.mkDerivation rec {
-  name = "pwndbg-2018-04-06";
+  name = "pwndbg-${version}";
+  version = "2018.07.29";

  src = fetchFromGitHub {
    owner = "pwndbg";
    repo = "pwndbg";
-    rev = "e225ba9f647ab8f7f4871075529c0ec239f43300";
-    sha256 = "1s6m93qi3baclgqqii4fnmzjmg0c6ipkscg7xiljaj5z4bs371j4";
+    rev = version;
+    sha256 = "1illk1smknaaa0ck8mwvig15c8al5w7fdp42a748xvm8wvxqxdsc";
  };

  nativeBuildInputs = [ makeWrapper ];
--- a/pkgs/development/tools/trellis/default.nix
+++ b/pkgs/development/tools/trellis/default.nix
@ -0,0 +1,49 @@
+{ stdenv, fetchFromGitHub, python3, cmake, boost }:
+
+let
+  trellisdb = fetchFromGitHub {
+    owner = "SymbiFlow";
+    repo  = "prjtrellis-db";
+    rev   = "06b429ddb7fd8ec1e3f2b35de2e94b4853cf2835";
+    sha256 = "07bsgw5x3gq0jcn9j4g7q9xvibvz6j2arjnvgyrxnrg30ri9q173";
+  };
+in
+stdenv.mkDerivation rec {
+  name = "trellis-${version}";
+  version = "2018.08.01";
+
+  buildInputs = [
+    (boost.override { python = python3; enablePython = true; })
+  ];
+
+  nativeBuildInputs = [
+    cmake python3
+  ];
+
+  src = fetchFromGitHub {
+    owner  = "SymbiFlow";
+    repo   = "prjtrellis";
+    rev    = "fff9532fe59bf9e38b44f029ce4a06c607a9ee78";
+    sha256 = "0ycw9fjf6428sf5x8x5szn8fha79610nf7nn8kmibgmz9868yv30";
+  };
+
+  preConfigure = ''
+    source environment.sh
+    cp -RT "${trellisdb}" database
+    cd libtrellis
+  '';
+
+  meta = {
+    description = "Documentation and tools for Lattice ECP5 FPGAs";
+    longDescription = ''
+      Project Trellis documents the Lattice ECP5 architecture
+      to enable development of open-source tools. Its goal is
+      to provide sufficient information to develop a free and
+      open Verilog to bitstream toolchain for these devices.
+    '';
+    homepage = https://github.com/SymbiFlow/prjtrellis;
+    license = stdenv.lib.licenses.isc;
+    maintainers = with stdenv.lib.maintainers; [ q3k ];
+    platforms = stdenv.lib.platforms.linux;
+  };
+}
--- a/pkgs/games/cataclysm-dda/common.nix
+++ b/pkgs/games/cataclysm-dda/common.nix
@ -0,0 +1,97 @@
+{ stdenv, fetchFromGitHub, pkgconfig, gettext, lua, ncurses
+, tiles, SDL2, SDL2_image, SDL2_mixer, SDL2_ttf, freetype, Cocoa
+, debug
+}:
+
+let
+  inherit (stdenv.lib) optionals;
+
+  cursesDeps = [ gettext lua ncurses ];
+
+  tilesDeps = [ SDL2 SDL2_image SDL2_mixer SDL2_ttf freetype ]
+    ++ optionals stdenv.isDarwin [ Cocoa ];
+
+  common = {
+    nativeBuildInputs = [ pkgconfig ];
+
+    buildInputs = cursesDeps ++ optionals tiles tilesDeps;
+
+    postPatch = ''
+      patchShebangs .
+    '';
+
+    makeFlags = [
+      "PREFIX=$(out)" "LUA=1" "USE_HOME_DIR=1" "LANGUAGES=all"
+    ] ++ optionals (!debug) [
+      "RELEASE=1"
+    ] ++ optionals tiles [
+      "TILES=1" "SOUND=1"
+    ] ++ optionals stdenv.isDarwin [
+      "NATIVE=osx" "CLANG=1"
+    ];
+
+    dontStrip = debug;
+
+    meta = with stdenv.lib; {
+      description = "A free, post apocalyptic, zombie infested rogue-like";
+      longDescription = ''
+        Cataclysm: Dark Days Ahead is a roguelike set in a post-apocalyptic world.
+        Surviving is difficult: you have been thrown, ill-equipped, into a
+        landscape now riddled with monstrosities of which flesh eating zombies are
+        neither the strangest nor the deadliest.
+
+        Yet with care and a little luck, many things are possible. You may try to
+        eke out an existence in the forests silently executing threats and
+        providing sustenance with your longbow. You can ride into town in a
+        jerry-rigged vehicle, all guns blazing, to settle matters in a fug of
+        smoke from your molotovs. You could take a more measured approach and
+        construct an impregnable fortress, surrounded by traps to protect you from
+        the horrors without. The longer you survive, the more skilled and adapted
+        you will get and the better equipped and armed to deal with the threats
+        you are presented with.
+
+        In the course of your ordeal there will be opportunities and temptations
+        to improve or change your very nature. There are tales of survivors fitted
+        with extraordinary cybernetics giving great power and stories too of
+        gravely mutated survivors who, warped by their ingestion of exotic
+        substances or radiation, now more closely resemble insects, birds or fish
+        than their original form.
+      '';
+      homepage = https://cataclysmdda.org/;
+      license = licenses.cc-by-sa-30;
+      maintainers = with maintainers; [ mnacamura ];
+      platforms = platforms.unix;
+    };
+  };
+
+  utils = {
+    fetchFromCleverRaven = { rev, sha256 }:
+    fetchFromGitHub {
+      owner = "CleverRaven";
+      repo = "Cataclysm-DDA";
+      inherit rev sha256;
+    };
+
+    installXDGAppLauncher = ''
+      launcher="$out/share/applications/cataclysm-dda.desktop"
+      install -D -m 444 data/xdg/com.cataclysmdda.cataclysm-dda.desktop -T "$launcher"
+      sed -i "$launcher" -e "s,\(Exec=\)\(cataclysm-tiles\),\1$out/bin/\2,"
+      install -D -m 444 data/xdg/cataclysm-dda.svg -t $out/share/icons/hicolor/scalable/apps
+    '';
+
+    installMacOSAppLauncher = ''
+      app=$out/Applications/Cataclysm.app
+      install -D -m 444 data/osx/Info.plist -t $app/Contents
+      install -D -m 444 data/osx/AppIcon.icns -t $app/Contents/Resources
+      mkdir $app/Contents/MacOS
+      launcher=$app/Contents/MacOS/Cataclysm.sh
+      cat << EOF > $launcher
+      #!${stdenv.shell}
+      $out/bin/cataclysm-tiles
+      EOF
+      chmod 555 $launcher
+    '';
+  };
+in
+
+{ inherit common utils; }
--- a/pkgs/games/cataclysm-dda/default.nix
+++ b/pkgs/games/cataclysm-dda/default.nix
@ -1,43 +1,30 @@
-{ fetchFromGitHub, stdenv, pkgconfig, ncurses, lua, SDL2, SDL2_image, SDL2_ttf,
-SDL2_mixer, freetype, gettext, Cocoa, libicns,
-tiles ? true }:
+{ stdenv, callPackage, ncurses
+, tiles ? true, Cocoa, libicns
+, debug ? false
+}:

-stdenv.mkDerivation rec {
+let
+  inherit (stdenv.lib) optionals optionalString;
+  inherit (callPackage ./common.nix { inherit tiles Cocoa debug; }) common utils;
+  inherit (utils) fetchFromCleverRaven installMacOSAppLauncher;
+in
+
+stdenv.mkDerivation (common // rec {
  version = "0.C";
  name = "cataclysm-dda-${version}";

-  src = fetchFromGitHub {
-    owner = "CleverRaven";
-    repo = "Cataclysm-DDA";
+  src = fetchFromCleverRaven {
    rev = "${version}";
    sha256 = "03sdzsk4qdq99qckq0axbsvg1apn6xizscd8pwp5w6kq2fyj5xkv";
  };

-  nativeBuildInputs = [ pkgconfig ]
-    ++ stdenv.lib.optionals (tiles && stdenv.isDarwin) [ libicns ];
-
-  buildInputs = with stdenv.lib; [ ncurses lua gettext ]
-    ++ optionals tiles [ SDL2 SDL2_image SDL2_ttf SDL2_mixer freetype ]
-    ++ optionals (tiles && stdenv.isDarwin) [ Cocoa ];
+  nativeBuildInputs = common.nativeBuildInputs
+    ++ optionals (tiles && stdenv.isDarwin) [ libicns ];

  patches = [ ./patches/fix_locale_dir.patch ];

-  postPatch = ''
-    patchShebangs .
-  '';
-
-  makeFlags = with stdenv.lib; [
-    "PREFIX=$(out)"
-    "LUA=1"
-    "RELEASE=1"
-    "USE_HOME_DIR=1"
-    # "LANGUAGES=all"  # vanilla C:DDA installs all translations even without this flag!
-  ] ++ optionals tiles [
-    "TILES=1"
-    "SOUND=1"
-  ] ++ optionals stdenv.isDarwin [
-    "NATIVE=osx"
-    "CLANG=1"
+  makeFlags = common.makeFlags
+    ++ optionals stdenv.isDarwin [
    "OSX_MIN=10.6"  # SDL for macOS only supports deploying on 10.6 and above
  ] ++ optionals stdenv.cc.isGNU [
    "WARNINGS+=-Wno-deprecated-declarations"
@ -46,57 +33,20 @@ stdenv.mkDerivation rec {
    "WARNINGS+=-Wno-inconsistent-missing-override"
  ];

-  NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.cc.isClang "-Wno-user-defined-warnings";
+  NIX_CFLAGS_COMPILE = optionalString stdenv.cc.isClang "-Wno-user-defined-warnings";

-  postBuild = stdenv.lib.optionalString (tiles && stdenv.isDarwin) ''
+  postBuild = optionalString (tiles && stdenv.isDarwin) ''
    # iconutil on macOS is not available in nixpkgs
    png2icns data/osx/AppIcon.icns data/osx/AppIcon.iconset/*
  '';

-  postInstall = stdenv.lib.optionalString (tiles && stdenv.isDarwin) ''
-    app=$out/Applications/Cataclysm.app
-    install -D -m 444 data/osx/Info.plist -t $app/Contents
-    install -D -m 444 data/osx/AppIcon.icns -t $app/Contents/Resources
-    mkdir $app/Contents/MacOS
-    launcher=$app/Contents/MacOS/Cataclysm.sh
-    cat << SCRIPT > $launcher
-    #!/bin/sh
-    $out/bin/cataclysm-tiles
-    SCRIPT
-    chmod 555 $launcher
-  '';
+  postInstall = optionalString (tiles && stdenv.isDarwin)
+    installMacOSAppLauncher;

  # Disable, possible problems with hydra
  #enableParallelBuilding = true;

-  meta = with stdenv.lib; {
-    description = "A free, post apocalyptic, zombie infested rogue-like";
-    longDescription = ''
-      Cataclysm: Dark Days Ahead is a roguelike set in a post-apocalyptic world.
-      Surviving is difficult: you have been thrown, ill-equipped, into a
-      landscape now riddled with monstrosities of which flesh eating zombies are
-      neither the strangest nor the deadliest.
-
-      Yet with care and a little luck, many things are possible. You may try to
-      eke out an existence in the forests silently executing threats and
-      providing sustenance with your longbow. You can ride into town in a
-      jerry-rigged vehicle, all guns blazing, to settle matters in a fug of
-      smoke from your molotovs. You could take a more measured approach and
-      construct an impregnable fortress, surrounded by traps to protect you from
-      the horrors without. The longer you survive, the more skilled and adapted
-      you will get and the better equipped and armed to deal with the threats
-      you are presented with.
-
-      In the course of your ordeal there will be opportunities and temptations
-      to improve or change your very nature. There are tales of survivors fitted
-      with extraordinary cybernetics giving great power and stories too of
-      gravely mutated survivors who, warped by their ingestion of exotic
-      substances or radiation, now more closely resemble insects, birds or fish
-      than their original form.
-    '';
-    homepage = https://cataclysmdda.org/;
-    license = licenses.cc-by-sa-30;
-    maintainers = [ maintainers.skeidel ];
-    platforms = platforms.unix;
+  meta = with stdenv.lib.maintainers; common.meta // {
+    maintainers = common.meta.maintainers ++ [ skeidel ];
  };
-}
+})
--- a/pkgs/games/cataclysm-dda/git.nix
+++ b/pkgs/games/cataclysm-dda/git.nix
@ -1,100 +1,44 @@
-{ fetchFromGitHub, stdenv, pkgconfig, ncurses, lua, SDL2, SDL2_image, SDL2_ttf,
-SDL2_mixer, freetype, gettext, CoreFoundation, Cocoa,
-tiles ? true, debug ? false }:
+{ stdenv, callPackage
+, tiles ? true, Cocoa, CoreFoundation
+, debug ? false
+}:

-stdenv.mkDerivation rec {
+let
+  inherit (stdenv.lib) optionals optionalString substring;
+  inherit (callPackage ./common.nix { inherit tiles Cocoa debug; }) common utils;
+  inherit (utils) fetchFromCleverRaven installXDGAppLauncher installMacOSAppLauncher;
+in
+
+stdenv.mkDerivation (common // rec {
  version = "2018-07-15";
  name = "cataclysm-dda-git-${version}";

-  src = fetchFromGitHub {
-    owner = "CleverRaven";
-    repo = "Cataclysm-DDA";
+  src = fetchFromCleverRaven {
    rev = "e1e5d81";
    sha256 = "198wfj8l1p8xlwicj92cq237pzv2ha9pcf240y7ijhjpmlc9jkr1";
  };

-  nativeBuildInputs = [ pkgconfig ];
-
-  buildInputs = with stdenv.lib; [ ncurses lua gettext ]
-    ++ optionals stdenv.isDarwin [ CoreFoundation ]
-    ++ optionals tiles [ SDL2 SDL2_image SDL2_ttf SDL2_mixer freetype ]
-    ++ optionals (tiles && stdenv.isDarwin) [ Cocoa ];
+  buildInputs = common.buildInputs
+    ++ optionals stdenv.isDarwin [ CoreFoundation ];

  patches = [ ./patches/fix_locale_dir_git.patch ];

-  postPatch = ''
-    patchShebangs .
-    sed -i data/xdg/com.cataclysmdda.cataclysm-dda.desktop \
-        -e "s,\(Exec=\)\(cataclysm-tiles\),\1$out/bin/\2,"
-  '';
-
-  makeFlags = with stdenv.lib; [
-    "PREFIX=$(out)"
-    "LUA=1"
-    "USE_HOME_DIR=1"
-    "LANGUAGES=all"
+  makeFlags = common.makeFlags ++ [
    "VERSION=git-${version}-${substring 0 8 src.rev}"
-  ] ++ optionals tiles [
-    "TILES=1"
-    "SOUND=1"
-  ] ++ optionals stdenv.isDarwin [
-    "NATIVE=osx"
-    "CLANG=1"
-  ] ++ optionals (! debug) [
-    "RELEASE=1"
  ];

-  postInstall = with stdenv.lib; optionalString (tiles && !stdenv.isDarwin) ''
-    install -D -m 444 data/xdg/com.cataclysmdda.cataclysm-dda.desktop -T $out/share/applications/cataclysm-dda.desktop
-    install -D -m 444 data/xdg/cataclysm-dda.svg -t $out/share/icons/hicolor/scalable/apps
-  '' + optionalString (tiles && stdenv.isDarwin) ''
-    app=$out/Applications/Cataclysm.app
-    install -D -m 444 data/osx/Info.plist -t $app/Contents
-    install -D -m 444 data/osx/AppIcon.icns -t $app/Contents/Resources
-    mkdir $app/Contents/MacOS
-    launcher=$app/Contents/MacOS/Cataclysm.sh
-    cat << SCRIPT > $launcher
-    #!/bin/sh
-    $out/bin/cataclysm-tiles
-    SCRIPT
-    chmod 555 $launcher
-  '';
+  postInstall = optionalString tiles
+  ( if !stdenv.isDarwin
+    then installXDGAppLauncher
+    else installMacOSAppLauncher
+  );

  # https://hydra.nixos.org/build/65193254
  # src/weather_data.cpp:203:1: fatal error: opening dependency file obj/tiles/weather_data.d: No such file or directory
  # make: *** [Makefile:687: obj/tiles/weather_data.o] Error 1
  enableParallelBuilding = false;

-  dontStrip = debug;
-
-  meta = with stdenv.lib; {
-    description = "A free, post apocalyptic, zombie infested rogue-like";
-    longDescription = ''
-      Cataclysm: Dark Days Ahead is a roguelike set in a post-apocalyptic world.
-      Surviving is difficult: you have been thrown, ill-equipped, into a
-      landscape now riddled with monstrosities of which flesh eating zombies are
-      neither the strangest nor the deadliest.
-
-      Yet with care and a little luck, many things are possible. You may try to
-      eke out an existence in the forests silently executing threats and
-      providing sustenance with your longbow. You can ride into town in a
-      jerry-rigged vehicle, all guns blazing, to settle matters in a fug of
-      smoke from your molotovs. You could take a more measured approach and
-      construct an impregnable fortress, surrounded by traps to protect you from
-      the horrors without. The longer you survive, the more skilled and adapted
-      you will get and the better equipped and armed to deal with the threats
-      you are presented with.
-
-      In the course of your ordeal there will be opportunities and temptations
-      to improve or change your very nature. There are tales of survivors fitted
-      with extraordinary cybernetics giving great power and stories too of
-      gravely mutated survivors who, warped by their ingestion of exotic
-      substances or radiation, now more closely resemble insects, birds or fish
-      than their original form.
-    '';
-    maintainers = with maintainers; [ rardiol ];
-    homepage = https://cataclysmdda.org/;
-    license = licenses.cc-by-sa-30;
-    platforms = platforms.unix;
+  meta = with stdenv.lib.maintainers; common.meta // {
+    maintainers = common.meta.maintainers ++ [ rardiol ];
  };
-}
+})
--- a/pkgs/servers/confluent/default.nix
+++ b/pkgs/servers/confluent/default.nix
@ -0,0 +1,49 @@
+{ stdenv, lib, fetchurl, jre, makeWrapper, bash, gnused }:
+
+with lib;
+
+let
+  confluentVersion = "4.1.1";
+  scalaVersion = "2.11";
+  sha256 = "e00eb4c6c7445ad7a43c9cd237778d1cd184322aebf5ff64a8e9806ba2cc27aa";
+in stdenv.mkDerivation rec {
+  name = "confluent-${version}";
+  version = "${confluentVersion}-${scalaVersion}";
+
+  src = fetchurl {
+    url = "http://packages.confluent.io/archive/${versions.majorMinor confluentVersion}/confluent-oss-${version}.tar.gz";
+    inherit sha256;
+  };
+
+  buildInputs = [ jre makeWrapper bash ];
+
+  installPhase = ''
+    mkdir -p $out
+    cp -R bin etc share src $out
+    rm -rf $out/bin/windows
+
+    patchShebangs $out/bin
+
+    # allow us the specify logging directory using env
+    substituteInPlace $out/bin/kafka-run-class \
+      --replace 'LOG_DIR="$base_dir/logs"' 'LOG_DIR="$KAFKA_LOG_DIR"'
+
+    substituteInPlace $out/bin/ksql-run-class \
+      --replace 'LOG_DIR="$base_dir/logs"' 'LOG_DIR="$KAFKA_LOG_DIR"'
+
+    for p in $out/bin\/*; do
+      wrapProgram $p \
+        --set JAVA_HOME "${jre}" \
+        --set KAFKA_LOG_DIR "/tmp/apache-kafka-logs" \
+        --prefix PATH : "${bash}/bin:${gnused}/bin"
+    done
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://www.confluent.io/;
+    description = "Confluent platform";
+    license = licenses.asl20;
+    maintainers = [ maintainers.offline ];
+    platforms = platforms.unix;
+  };
+}
--- a/pkgs/servers/dns/knot-resolver/default.nix
+++ b/pkgs/servers/dns/knot-resolver/default.nix
@ -12,11 +12,11 @@ inherit (stdenv.lib) optional concatStringsSep;

 unwrapped = stdenv.mkDerivation rec {
  name = "knot-resolver-${version}";
-  version = "2.4.0";
+  version = "2.4.1";

  src = fetchurl {
    url = "https://secure.nic.cz/files/knot-resolver/${name}.tar.xz";
-    sha256 = "8c88c73dd50dad6f371bfc170f49cd374022e59f8005ac1fa6cd99764f72b4d1";
+    sha256 = "e8044316cd897ad29b3c5284de06652e1568c4d5861e3147ec2191fbacd8d9ff";
  };

  outputs = [ "out" "dev" ];
--- a/pkgs/servers/freeradius/default.nix
+++ b/pkgs/servers/freeradius/default.nix
@ -21,6 +21,8 @@
 , withYubikey ? false
 , collectd
 , withCollectd ? false
+, curl
+, withRest ? false
 }:

 assert withSqlite -> sqlite != null;
@ -32,6 +34,7 @@ assert withRedis -> hiredis != null;
 assert withMysql -> mysql != null;
 assert withYubikey -> libyubikey != null;
 assert withCollectd -> collectd != null;
+assert withRest -> curl != null && withJson;

 ## TODO: include windbind optionally (via samba?)
 ## TODO: include oracle optionally
@ -59,11 +62,13 @@ stdenv.mkDerivation rec {
    ++ optional withMysql mysql.connector-c
    ++ optional withJson json_c
    ++ optional withYubikey libyubikey
-    ++ optional withCollectd collectd;
+    ++ optional withCollectd collectd
+    ++ optional withRest curl;
+

  configureFlags = [
-     "--sysconfdir=/etc"
-     "--localstatedir=/var"
+    "--sysconfdir=/etc"
+    "--localstatedir=/var"
  ] ++ optional (!linkOpenssl) "--with-openssl=no";

  postPatch = ''
@ -75,6 +80,8 @@ stdenv.mkDerivation rec {
    "localstatedir=\${TMPDIR}"
  ];

+  outputs = [ "out" "dev" "man" "doc" ];
+
  meta = with stdenv.lib; {
    homepage = https://freeradius.org/;
    description = "A modular, high performance free RADIUS suite";
--- a/pkgs/servers/plex/default.nix
+++ b/pkgs/servers/plex/default.nix
@ -6,9 +6,9 @@
 let
  plexPass = throw "Plex pass has been removed at upstream's request; please unset nixpkgs.config.plex.pass";
  plexpkg = if enablePlexPass then plexPass else {
-    version = "1.13.0.5023";
-    vsnHash = "31d3c0c65";
-    sha256 = "b94d571bcd47bc3201fd7f54b910f5693cabd1b543d5d0b4705668b7b7c24602";
+    version = "1.13.4.5271";
+    vsnHash = "200287a06";
+    sha256 = "c8aa459f680ad9db92f285dae2f3dcffbf082324e1b7ea2f356bdbe745fe6b8e";
  };

 in stdenv.mkDerivation rec {
--- a/pkgs/servers/sql/mariadb/default.nix
+++ b/pkgs/servers/sql/mariadb/default.nix
@ -22,14 +22,14 @@ galeraLibs = buildEnv {
 };

 common = rec { # attributes common to both builds
-  version = "10.2.16";
+  version = "10.3.8";

  src = fetchurl {
    urls = [
      "https://downloads.mariadb.org/f/mariadb-${version}/source/mariadb-${version}.tar.gz"
      "https://downloads.mariadb.com/MariaDB/mariadb-${version}/source/mariadb-${version}.tar.gz"
    ];
-    sha256 = "1i2dwpp96ywjk147qqpcad8vqcy4rxmfbv2cb8ww3sffpa9yx0n1";
+    sha256 = "1f0syfrv0my7sm8cbpic00ldy90psimy8yvm0ld82bfi2isw3gih";
    name   = "mariadb-${version}.tar.gz";
  };

--- a/pkgs/tools/archivers/cabextract/default.nix
+++ b/pkgs/tools/archivers/cabextract/default.nix
@ -1,11 +1,11 @@
 { stdenv, fetchurl }:

 stdenv.mkDerivation rec {
-  name = "cabextract-1.6";
+  name = "cabextract-1.7";

  src = fetchurl {
    url = "https://www.cabextract.org.uk/${name}.tar.gz";
-    sha256 = "1ysmmz25fjghq7mxb2anyyvr1ljxqxzi4piwjhk0sdamcnsn3rnf";
+    sha256 = "1g86wmb8lkjiv2jarfz979ngbgg7d3si8x5il4g801604v406wi9";
  };

  meta = with stdenv.lib; {
--- a/pkgs/tools/audio/abcm2ps/default.nix
+++ b/pkgs/tools/audio/abcm2ps/default.nix
@ -2,13 +2,13 @@

 stdenv.mkDerivation rec {
  name = "abcm2ps-${version}";
-  version = "8.13.23";
+  version = "8.13.24";

  src = fetchFromGitHub {
    owner = "leesavide";
    repo = "abcm2ps";
    rev = "v${version}";
-    sha256 = "00bc4vsdvnyznfwcrkij02n2736nsbjlrh0rng96zv00p4abv4ad";
+    sha256 = "0xb0gdxbagy6bzrh61s667svab43r06d6yi20gw52dh022mj99ag";
  };

  prePatch = ''
@ -23,7 +23,9 @@ stdenv.mkDerivation rec {
    "CC=${stdenv.cc}/bin/cc"
  ];

-  buildInputs = [ which pkgconfig freetype pango ];
+  nativeBuildInputs = [ which pkgconfig ];
+
+  buildInputs = [ freetype pango ];

  meta = with stdenv.lib; {
    homepage = http://moinejf.free.fr/;
--- a/pkgs/tools/audio/beets/alternatives-beets-1.4.6.patch
+++ b/pkgs/tools/audio/beets/alternatives-beets-1.4.6.patch
@ -1,30 +0,0 @@
-diff --git a/test/helper.py b/test/helper.py
-index c216226..d409c09 100644
--- a/test/helper.py
-+++ b/test/helper.py
-@@ -11,6 +11,7 @@ import beets
- from beets import plugins
- from beets import ui
- from beets.library import Item
-+from beets.util import MoveOperation
- 
- from beetsplug import alternatives
- from beetsplug import convert
-@@ -183,7 +184,7 @@ class TestHelper(Assertions):
-         item = Item.from_path(os.path.join(self.fixture_dir, 'min.' + ext))
-         item.add(self.lib)
-         item.update(values)
-        item.move(copy=True)
-+        item.move(operation=MoveOperation.COPY)
-         item.write()
-         album = self.lib.add_album([item])
-         album.albumartist = item.artist
-@@ -201,7 +202,7 @@ class TestHelper(Assertions):
-         item = Item.from_path(os.path.join(self.fixture_dir, 'min.mp3'))
-         item.add(self.lib)
-         item.update(values)
-        item.move(copy=True)
-+        item.move(operation=MoveOperation.COPY)
-         item.write()
-         return item
- 
--- a/pkgs/tools/audio/beets/alternatives-plugin.nix
+++ b/pkgs/tools/audio/beets/alternatives-plugin.nix
@ -6,24 +6,20 @@ pythonPackages.buildPythonApplication rec {

  src = fetchFromGitHub {
    repo = "beets-alternatives";
-    owner = "geigerzaehler";
-    rev = "v${version}";
-    sha256 = "10za6h59pxa13y8i4amqhc6392csml0dl771lssv6b6a98kamsy7";
+    owner = "wisp3rwind";
+    # This is 0.8.2 with fixes against Beets 1.4.6 and Python 3 compatibility.
+    rev = "331eb406786a2d4dc3dd721a534225b087474b1e";
+    sha256 = "1avds2x5sp72c89l1j52pszprm85g9sm750jh1dhnyvgcbk91cb5";
  };

-  patches = [ ./alternatives-beets-1.4.6.patch ];
-
  postPatch = ''
-    sed -i -e '/install_requires/,/\]/{/beets/d}' setup.py
-    sed -i -e '/test_suite/d' setup.py
+    sed -i -e '/long_description/d' setup.py
  '';

  nativeBuildInputs = [ beets pythonPackages.nose ];

  checkPhase = "nosetests";

-  propagatedBuildInputs = with pythonPackages; [ futures ];
-
  meta = {
    description = "Beets plugin to manage external files";
    homepage = https://github.com/geigerzaehler/beets-alternatives;
--- a/pkgs/tools/audio/beets/copyartifacts-plugin.nix
+++ b/pkgs/tools/audio/beets/copyartifacts-plugin.nix
@ -6,8 +6,8 @@ pythonPackages.buildPythonApplication rec {
  src = fetchFromGitHub {
    repo = "beets-copyartifacts";
    owner = "sbarakat";
-    rev = "4a5d347c858d25641c8a0eb7d8cb1a2cac10252a";
-    sha256 = "0bn6fci480ilghrdhpsjxxq29dxgni22sv1qalz770xy130g1zk3";
+    rev = "d0bb75c8fc8fe125e8191d73de7ade6212aec0fd";
+    sha256 = "19b4lqq1p45n348ssmql60jylw2fw7vfj9j22nly5qj5qx51j3g5";
  };

  postPatch = ''
--- a/pkgs/tools/audio/beets/default.nix
+++ b/pkgs/tools/audio/beets/default.nix
@ -91,9 +91,11 @@ let
    doInstallCheck = false;
  });

+  pluginArgs = externalTestArgs // { inherit pythonPackages; };
+
  plugins = {
-    alternatives = callPackage ./alternatives-plugin.nix externalTestArgs;
-    copyartifacts = callPackage ./copyartifacts-plugin.nix externalTestArgs;
+    alternatives = callPackage ./alternatives-plugin.nix pluginArgs;
+    copyartifacts = callPackage ./copyartifacts-plugin.nix pluginArgs;
  };

 in pythonPackages.buildPythonApplication rec {
--- a/pkgs/tools/misc/coreutils/default.nix
+++ b/pkgs/tools/misc/coreutils/default.nix
@ -100,7 +100,7 @@ stdenv.mkDerivation rec {

    license = licenses.gpl3Plus;

-    platforms = platforms.all;
+    platforms = platforms.unix;

    maintainers = [ maintainers.eelco ];
  };
--- a/pkgs/tools/networking/ocserv/default.nix
+++ b/pkgs/tools/networking/ocserv/default.nix
@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitLab, autoreconfHook, pkgconfig, nettle, gnutls
+, libev, protobufc, guile, geoip, libseccomp, gperf, readline
+, lz4, libgssglue, ronn, coreutils, pam
+}:
+
+stdenv.mkDerivation rec {
+  name = "ocserv-${version}";
+  version = "0.12.1";
+
+  src = fetchFromGitLab {
+    owner = "openconnect";
+    repo = "ocserv";
+    rev = "ocserv_${stdenv.lib.replaceStrings [ "." ] [ "_" ] version}";
+    sha256 = "0jn91a50r3ryj1ph9fzxwy2va877b0b37ahargxzn7biccd8nh0y";
+  };
+
+  nativeBuildInputs = [ autoreconfHook pkgconfig ];
+  buildInputs = [ nettle gnutls libev protobufc guile geoip libseccomp gperf readline lz4 libgssglue ronn pam ];
+
+  meta = with stdenv.lib; {
+    homepage = https://gitlab.com/openconnect/ocserv;
+    license = licenses.gpl2;
+    description = "This program is openconnect VPN server (ocserv), a server for the openconnect VPN client.";
+    maintainers = with maintainers; [ ma27 ];
+  };
+}
--- a/pkgs/tools/networking/photon/default.nix
+++ b/pkgs/tools/networking/photon/default.nix
@ -0,0 +1,40 @@
+{ stdenv, pythonPackages, fetchurl, makeWrapper }:
+
+with pythonPackages;
+buildPythonApplication rec {
+  pname = "photon";
+  version = "1.0.7";
+
+  src = fetchurl {
+    url = "https://github.com/s0md3v/Photon/archive/v${version}.tar.gz";
+    sha256 = "0c5l1sbkkagfxmh8v7yvi6z58mhqbwjyr7fczb5qwxm7la42ah9y";
+  };
+
+  patches = [ ./destdir.patch ];
+  postPatch = ''
+       substituteInPlace photon.py --replace DESTDIR $out/share/photon 
+  '';
+
+  dontBuild = true;
+  doCheck = false;
+  propagatedBuildInputs = [
+    requests
+    urllib3
+  ];
+
+  installPhase = ''
+    mkdir -p "$out"/{bin,share/photon}
+    cp -R photon.py core plugins $out/share/photon
+ 
+    makeWrapper ${python.interpreter} $out/bin/photon \
+      --set PYTHONPATH "$PYTHONPATH:$out/share/photon" \
+      --add-flags "-O $out/share/photon/photon.py"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "a lightning fast web crawler which extracts URLs, files, intel & endpoints from a target";
+    homepage = https://github.com/s0md3v/Photon;
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ genesis ];
+  };
+}
--- a/pkgs/tools/networking/photon/destdir.patch
+++ b/pkgs/tools/networking/photon/destdir.patch
@ -0,0 +1,20 @@
+diff --git a/photon.py.old b/photon.py
+index 92498e4..f7e2c3d 100644
+--- a/photon.py.old
+++ b/photon.py
+@@ -185,7 +185,7 @@ if args.user_agent:
+     user_agents = args.user_agent.split(',')
+ else:
+     user_agents = []
+-    with open(os.getcwd() + '/core/user-agents.txt', 'r') as uas:
+    with open('DESTDIR/core/user-agents.txt', 'r') as uas:
+         for agent in uas:
+             user_agents.append(agent.strip('\n'))
+ 
+@@ -534,4 +534,4 @@ if args.export:
+ if not colors: # if colors are disabled
+     print ('%s Results saved in %s directory' % (good, output_dir))
+ else:
+-    print ('%s Results saved in \033[;1m%s\033[0m directory' % (good, output_dir))
+\ No newline at end of file
+    print ('%s Results saved in \033[;1m%s\033[0m directory' % (good, output_dir))
--- a/pkgs/tools/networking/tinyproxy/default.nix
+++ b/pkgs/tools/networking/tinyproxy/default.nix
@ -0,0 +1,56 @@
+{ stdenv, fetchFromGitHub, automake, autoreconfHook, asciidoc, libxml2,
+  libxslt, docbook_xsl }:
+
+stdenv.mkDerivation rec{
+  name = "tinyproxy-${version}";
+  version = "1.8.4";
+
+  src = fetchFromGitHub {
+    sha256 = "043mfqin5bsba9igm1lqbkp2spibk4j3niyjqc868cnzgx60709c";
+    rev = "${version}";
+    repo = "tinyproxy";
+    owner = "tinyproxy";
+  };
+
+  nativeBuildInputs = [ autoreconfHook asciidoc libxml2 libxslt docbook_xsl ];
+
+  # -z flag is not supported in darwin
+  preAutoreconf = stdenv.lib.optionalString stdenv.isDarwin ''
+    substituteInPlace configure.ac --replace \
+          'LDFLAGS="-Wl,-z,defs $LDFLAGS"' \
+          'LDFLAGS="-Wl, $LDFLAGS"'
+  '';
+
+  # See: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=154624
+  postConfigure = ''
+    substituteInPlace docs/man5/Makefile --replace \
+          "-f manpage" \
+          "--xsltproc-opts=--nonet \\
+           -f manpage \\
+           -L"
+    substituteInPlace docs/man8/Makefile --replace \
+          "-f manpage" \
+          "--xsltproc-opts=--nonet \\
+           -f manpage \\
+           -L"
+  '';
+
+  configureFlags = [
+    "--disable-debug"      # Turn off debugging
+    "--enable-xtinyproxy"  # Compile in support for the XTinyproxy header, which is sent to any web server in your domain.
+    "--enable-filter"      # Allows Tinyproxy to filter out certain domains and URLs.
+    "--enable-upstream"    # Enable support for proxying connections through another proxy server.
+    "--enable-transparent" # Allow Tinyproxy to be used as a transparent proxy daemon.
+    "--enable-reverse"     # Enable reverse proxying.
+  ] ++
+  # See: https://github.com/tinyproxy/tinyproxy/issues/1
+  stdenv.lib.optional stdenv.isDarwin "--disable-regexcheck";
+
+  meta = with stdenv.lib; {
+    homepage = https://tinyproxy.github.io/;
+    description = "A light-weight HTTP/HTTPS proxy daemon for POSIX operating systems";
+    license = licenses.gpl2;
+    platforms = platforms.all;
+    maintainers = [ maintainers.carlosdagos ];
+  };
+}
--- a/pkgs/tools/package-management/cargo-update/cargo-update.nix
+++ b/pkgs/tools/package-management/cargo-update/cargo-update.nix
--- a/pkgs/tools/package-management/cargo-update/default.nix
+++ b/pkgs/tools/package-management/cargo-update/default.nix
@ -0,0 +1,27 @@
+{ stdenv, callPackage, defaultCrateOverrides, fetchFromGitHub, cmake, libssh2, libgit2, openssl, zlib }:
+
+((callPackage ./cargo-update.nix {}).cargo_update {}).override {
+  crateOverrides = defaultCrateOverrides // {
+    cargo-update = attrs: rec {
+      name = "cargo-update-${version}";
+      version = "1.5.2";
+
+      src = fetchFromGitHub {
+        owner = "nabijaczleweli";
+        repo = "cargo-update";
+        rev = "v${version}";
+        sha256 = "1bvrdgcw2akzd78wgvsisvghi8pvdk3szyg9s46qxv4km9sf88s7";
+      };
+
+      buildInputs = [ cmake libssh2 libgit2 openssl zlib ];
+
+      meta = with stdenv.lib; {
+        description = "A cargo subcommand for checking and applying updates to installed executables";
+        homepage = https://github.com/nabijaczleweli/cargo-update;
+        license = with licenses; [ mit ];
+        maintainers = with maintainers; [ gerschtli ];
+        platforms = platforms.all;
+      };
+    };
+  };
+}
--- a/pkgs/tools/text/proselint/default.nix
+++ b/pkgs/tools/text/proselint/default.nix
@ -2,13 +2,13 @@

 buildPythonApplication rec {
  name = "proselint-${version}";
-  version = "0.9.0";
+  version = "0.10.0";

  doCheck = false; # fails to pass because it tries to run in home directory

  src = fetchurl {
    url = "mirror://pypi/p/proselint/${name}.tar.gz";
-    sha256 = "1fibk24fx00bfn0z4iikcv519cz2nkcil9k187sf3adb2ldzg4ab";
+    sha256 = "0kmr95mf2gij40qy4660ryfanw13vxlhpmivqia1mdbii8iziyhg";
  };

  propagatedBuildInputs = [ click future six ];
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -670,6 +670,8 @@ with pkgs;

  gitless = callPackage ../applications/version-management/gitless { };

+  gitter = callPackage  ../applications/networking/instant-messengers/gitter { };
+
  grc = callPackage ../tools/misc/grc { };

  green-pdfviewer = callPackage ../applications/misc/green-pdfviewer {
@ -1322,6 +1324,8 @@ with pkgs;

  glide = callPackage ../development/tools/glide { };

+  globalarrays = callPackage ../development/libraries/globalarrays { };
+
  glock = callPackage ../development/tools/glock { };

  glslviewer = callPackage ../development/tools/glslviewer {
@ -1442,6 +1446,8 @@ with pkgs;

  pbzx = callPackage ../tools/compression/pbzx { };

+  photon = callPackage ../tools/networking/photon { };
+
  playerctl = callPackage ../tools/audio/playerctl { };

  ps_mem = callPackage ../tools/system/ps_mem { };
@ -2725,6 +2731,8 @@ with pkgs;
    inherit (gnome2) gnome_python gnome_python_desktop;
  };

+  gnome-builder = callPackage ../applications/editors/gnome-builder { };
+
  gnokii = callPackage ../tools/misc/gnokii { };

  gnuapl = callPackage ../development/interpreters/gnu-apl { };
@ -4250,6 +4258,8 @@ with pkgs;

  ocproxy = callPackage ../tools/networking/ocproxy { };

+  ocserv = callPackage ../tools/networking/ocserv { };
+
  openfortivpn = callPackage ../tools/networking/openfortivpn { };

  obexfs = callPackage ../tools/bluetooth/obexfs { };
@ -5442,6 +5452,8 @@ with pkgs;

  tiny8086 = callPackage ../applications/virtualization/8086tiny { };

+  tinyproxy = callPackage ../tools/networking/tinyproxy {};
+
  tio = callPackage ../tools/misc/tio { };

  tldr = callPackage ../tools/misc/tldr { };
@ -7081,6 +7093,7 @@ with pkgs;
  cargo-edit = callPackage ../tools/package-management/cargo-edit { };
  cargo-release = callPackage ../tools/package-management/cargo-release { };
  cargo-tree = callPackage ../tools/package-management/cargo-tree { };
+  cargo-update = callPackage ../tools/package-management/cargo-update { };

  cargo-asm = callPackage ../development/tools/rust/cargo-asm { };
  cargo-fuzz = callPackage ../development/tools/rust/cargo-fuzz { };
@ -7968,6 +7981,8 @@ with pkgs;

  corundum = callPackage ../development/tools/corundum { };

+  confluent = callPackage ../servers/confluent {};
+
  ctags = callPackage ../development/tools/misc/ctags { };

  ctagsWrapped = callPackage ../development/tools/misc/ctags/wrapped.nix {};
@ -8614,6 +8629,8 @@ with pkgs;

  travis = callPackage ../development/tools/misc/travis { };

+  trellis = callPackage ../development/tools/trellis { };
+
  tweak = callPackage ../applications/editors/tweak { };

  uhd = callPackage ../development/tools/misc/uhd { };
@ -11420,6 +11437,8 @@ with pkgs;

  pugixml = callPackage ../development/libraries/pugixml { };

+  pybind11 = callPackage ../development/libraries/pybind11 { };
+
  re2 = callPackage ../development/libraries/re2 { };

  qbs = callPackage ../development/tools/build-managers/qbs { };
@ -15181,7 +15200,8 @@ with pkgs;

  amsn = callPackage ../applications/networking/instant-messengers/amsn { };

-  androidStudioPackages = callPackage ../applications/editors/android-studio { };
+  androidStudioPackages = recurseIntoAttrs
+    (callPackage ../applications/editors/android-studio { });
  android-studio = androidStudioPackages.stable;
  android-studio-preview = androidStudioPackages.beta;

@ -20301,6 +20321,8 @@ with pkgs;

  octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; };

+  openmolcas = callPackage ../applications/science/chemistry/openmolcas { };
+
  pymol = callPackage ../applications/science/chemistry/pymol { };

  ### SCIENCE/GEOMETRY
@ -20414,6 +20436,8 @@ with pkgs;

  snpeff = callPackage ../applications/science/biology/snpeff { };

+  somatic-sniper = callPackage ../applications/science/biology/somatic-sniper { };
+
  star = callPackage ../applications/science/biology/star { };

  varscan = callPackage ../applications/science/biology/varscan { };
@ -22022,4 +22046,5 @@ with pkgs;

  powershell = callPackage ../shells/powershell { };

+  doing = callPackage ../applications/misc/doing  { };
 }
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@ -69,8 +69,6 @@ let
  # See build-setupcfg/default.nix for documentation.
  buildSetupcfg = import ../build-support/build-setupcfg self;

-  graphiteVersion = "1.0.2";
-
  fetchPypi = makeOverridable( {format ? "setuptools", ... } @attrs:
    let
      fetchWheel = {pname, version, sha256, python ? "py2.py3", abi ? "none", platform ? "any"}:
@ -340,12 +338,16 @@ in {

  outcome = callPackage ../development/python-modules/outcome {};

+  palettable = callPackage ../development/python-modules/palettable { };
+
  pdf2image = callPackage ../development/python-modules/pdf2image { };

  pdfminer = callPackage ../development/python-modules/pdfminer_six { };

  pdfx = callPackage ../development/python-modules/pdfx { };

+  phonopy = callPackage ../development/python-modules/phonopy { };
+
  plantuml = callPackage ../tools/misc/plantuml { };

  Pmw = callPackage ../development/python-modules/Pmw { };
@ -420,6 +422,8 @@ in {
  };

  pykerberos = callPackage ../development/python-modules/pykerberos { };
+  
+  pymatgen = callPackage ../development/python-modules/pymatgen { };

  pynisher = callPackage ../development/python-modules/pynisher { };

@ -499,6 +503,8 @@ in {

  spglib = callPackage ../development/python-modules/spglib { };

+  sumo = callPackage ../development/python-modules/sumo { };
+
  supervise_api = callPackage ../development/python-modules/supervise_api { };

  syncserver = callPackage ../development/python-modules/syncserver {};
@ -4774,13 +4780,14 @@ in {
  django_tagging = callPackage ../development/python-modules/django_tagging { };

  django_tagging_0_4_3 = if
-       self.django != self.django_1_8
+       self.django.version != "1.8.18"
  then throw "django_tagging_0_4_3 should be build with django_1_8"
  else (callPackage ../development/python-modules/django_tagging {}).overrideAttrs (attrs: rec {
-    name = "django-tagging-0.4.3";
+    pname = "django-tagging";
+    version = "0.4.3";

-    src = pkgs.fetchurl {
-      url = "mirror://pypi/d/django-tagging/${name}.tar.gz";
+    src = fetchPypi {
+      inherit pname version;
      sha256 = "0617azpmp6jpg3d88v2ir97qrc9aqcs2s9gyvv9bgf2cp55khxhs";
    };
    propagatedBuildInputs = with self; [ django ];
@ -15393,24 +15400,7 @@ EOF

  whichcraft = callPackage ../development/python-modules/whichcraft { };

-  whisper = buildPythonPackage rec {
-    name = "whisper-${version}";
-    version = graphiteVersion;
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/w/whisper/${name}.tar.gz";
-      sha256 = "1v1bi3fl1i6p4z4ki692bykrkw6907dn3mfq0151f70lvi3zpns3";
-    };
-
-    # error: invalid command 'test'
-    doCheck = false;
-
-    meta = {
-      homepage = http://graphite.wikidot.com/;
-      description = "Fixed size round-robin style database";
-      maintainers = with maintainers; [ rickynils offline ];
-    };
-  };
+  whisper = callPackage ../development/python-modules/whisper { };

  worldengine = buildPythonPackage rec {
    name = "worldengine-${version}";
@ -15460,27 +15450,7 @@ EOF
    };
  };

-  carbon = buildPythonPackage rec {
-    name = "carbon-${version}";
-    version = graphiteVersion;
-
-    disabled = isPy3k;
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/c/carbon/${name}.tar.gz";
-      sha256 = "142smpmgbnjinvfb6s4ijazish4vfgzyd8zcmdkh55y051fkixkn";
-    };
-
-    propagatedBuildInputs = with self; [ whisper txamqp zope_interface twisted ];
-
-    meta = {
-      homepage = http://graphite.wikidot.com/;
-      description = "Backend data caching and persistence daemon for Graphite";
-      maintainers = with maintainers; [ rickynils offline ];
-      license = licenses.asl20;
-    };
-  };
-
+  carbon = callPackage ../development/python-modules/carbon { };

  ujson = buildPythonPackage rec {
    name = "ujson-1.35";
@ -15608,126 +15578,15 @@ EOF
    };
  };

-  graphite_web = if
-          self.django != self.django_1_8
-       || self.django_tagging != self.django_tagging_0_4_3
-  then throw "graphite_web should be build with django_1_8 and django_tagging_0_4_3"
-  else buildPythonPackage rec {
-    name = "graphite-web-${version}";
-    disabled = isPy3k;
-    version = graphiteVersion;
-
-    src = pkgs.fetchurl rec {
-      url = "mirror://pypi/g/graphite-web/${name}.tar.gz";
-      sha256 = "0q8bwlj75jqyzmazfsi5sa26xl58ssa8wdxm2l4j0jqyn8xpfnmc";
-    };
-
-    propagatedBuildInputs = with self; [
-      django django_tagging whisper pycairo cairocffi
-      ldap memcached pytz urllib3 scandir
-    ];
-
-    postInstall = ''
-      wrapProgram $out/bin/run-graphite-devel-server.py \
-        --prefix PATH : ${pkgs.which}/bin
-    '';
-
-    preConfigure = ''
-      # graphite is configured by storing a local_settings.py file inside the
-      # graphite python package. Since that package is stored in the immutable
-      # Nix store we can't modify it. So how do we configure graphite?
-      #
-      # First of all we rename "graphite.local_settings" to
-      # "graphite_local_settings" so that the settings are not looked up in the
-      # graphite package anymore. Secondly we place a directory containing a
-      # graphite_local_settings.py on the PYTHONPATH in the graphite module
-      # <nixpkgs/nixos/modules/services/monitoring/graphite.nix>.
-      substituteInPlace webapp/graphite/settings.py \
-        --replace "graphite.local_settings" " graphite_local_settings"
-
-      substituteInPlace webapp/graphite/settings.py \
-        --replace "join(WEBAPP_DIR, 'content')" "join('$out', 'webapp', 'content')"
-    '';
-
-    # error: invalid command 'test'
-    doCheck = false;
-
-    meta = {
-      homepage = http://graphite.wikidot.com/;
-      description = "Enterprise scalable realtime graphing";
-      maintainers = with maintainers; [ rickynils offline ];
-    };
-  };
+  graphite-web = callPackage ../development/python-modules/graphite-web { };

  graphite_api = callPackage ../development/python-modules/graphite-api { };

-  graphite_beacon = buildPythonPackage rec {
-    name = "graphite_beacon-0.27.0";
+  graphite_beacon = callPackage ../development/python-modules/graphite_beacon { };

-    src = pkgs.fetchurl {
-      url = "mirror://pypi/g/graphite_beacon/${name}.tar.gz";
-      sha256 = "03bp4wyfn3xhcqyvs5hnk1n87m4smsmm1p7qp459m7j8hwpbq2ks";
-    };
-
-    propagatedBuildInputs = [ self.tornado self.pyyaml self.funcparserlib ];
-
-    preBuild = "> requirements.txt";
-
-    meta = {
-      description = "A simple alerting application for Graphite metrics";
-      homepage = https://github.com/klen/graphite-beacon;
-      maintainers = [ maintainers.offline ];
-      license = licenses.mit;
-    };
-  };
-
-  graphite_influxdb = buildPythonPackage rec {
-    name = "graphite-influxdb-0.3";
-
-    src = pkgs.fetchgit {
-      url = "https://github.com/vimeo/graphite-influxdb.git";
-      rev = "2273d12a24e1d804685a36debfd4224b7416b62f";
-      sha256 = "1v00fgrnmsd9c0ahggyw9sia5m7dyzz16i5pa4vy6w2sbfyrmm4v";
-    };
-
-    propagatedBuildInputs = with self; [ influxdb graphite_api ];
-
-    passthru.moduleName = "graphite_influxdb.InfluxdbFinder";
-
-    meta = {
-      description = "An influxdb backend for Graphite-web and graphite-api";
-      homepage = https://github.com/vimeo/graphite-influxdb;
-      license = licenses.asl20;
-    };
-  };
-
-  graphite_pager = buildPythonPackage rec {
-    name = "graphite-pager-${version}";
-    version = "2bbfe91220ec1e0ca1cdf4b5564386482a44ed7d";
-
-    src = pkgs.fetchgit {
-      url = "https://github.com/offlinehacker/graphite-pager.git";
-      sha256 = "0ylal0vkc2yrjvssfz1gls84yk9vkvvkx3pyv4lx15jm2qqzdmxd";
-      rev = version;
-    };
-
-    buildInputs = with self; [ nose mock ];
-    propagatedBuildInputs = with self; [
-      jinja2 pyyaml redis requests pagerduty
-      python-simple-hipchat pushbullet
-    ];
-
-    patchPhase = "> requirements.txt";
-    checkPhase = "nosetests";
-
-    meta = {
-      description = "A simple alerting application for Graphite metrics";
-      homepage = https://github.com/seatgeek/graphite-pager;
-      maintainers = with maintainers; [ offline ];
-      license = licenses.bsd2;
-    };
-  };
+  influxgraph = callPackage ../development/python-modules/influxgraph { };

+  graphitepager = callPackage ../development/python-modules/graphitepager { };

  pyspotify = buildPythonPackage rec {
    name = "pyspotify-${version}";