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

.github/CODEOWNERS

@@ -7,17 +7,34 @@
 # For documentation on this file, see https://help.github.com/articles/about-codeowners/
 # Mentioned users will get code review requests.
 
-# Python-related code and docs
-pkgs/top-level/python-packages.nix	@FRidh
-pkgs/development/interpreters/python/*	@FRidh
-pkgs/development/python-modules/*	@FRidh
-doc/languages-frameworks/python.md	@FRidh
-
 # Boostraping and core infra
-pkgs/stdenv/	@Ericson2314
-pkgs/build-support/cc-wrapper/	@Ericson2314
+pkgs/stdenv/    @Ericson2314
+pkgs/build-support/cc-wrapper/  @Ericson2314
+
+# Libraries
+lib/  @Profpatsch
+
+# Build-Support
+pkgs/build-support  @Profpatsch
+
+# Python-related code and docs
+pkgs/top-level/python-packages.nix      @FRidh
+pkgs/development/interpreters/python/*  @FRidh
+pkgs/development/python-modules/*       @FRidh
+doc/languages-frameworks/python.md      @FRidh
+
+# Haskell
+pkgs/development/compilers/ghc                       @peti
+pkgs/development/haskell-modules                     @peti
+pkgs/development/haskell-modules/default.nix         @Profpatsch @peti
+pkgs/development/haskell-modules/generic-builder.nix @Profpatsch @peti
+pkgs/development/haskell-modules/hoogle.nix          @Profpatsch @peti
+
+# R
+pkgs/applications/science/math/R @peti
+pkgs/development/r-modules       @peti
 
 # Darwin-related
-pkgs/stdenv/darwin/*	@copumpkin @LnL7
-pkgs/os-specific/darwin/*	@LnL7
-pkgs/os-specific/darwin/apple-source-releases/*	@copumpkin
+pkgs/stdenv/darwin/*    @copumpkin @LnL7
+pkgs/os-specific/darwin/*       @LnL7
+pkgs/os-specific/darwin/apple-source-releases/* @copumpkin

lib/maintainers.nix

@@ -577,6 +577,7 @@
   tavyc = "Octavian Cerna <octavian.cerna@gmail.com>";
   ltavard = "Laure Tavard <laure.tavard@univ-grenoble-alpes.fr>";
   teh = "Tom Hunger <tehunger@gmail.com>";
+  teto = "Matthieu Coudron <mcoudron@hotmail.com>";
   telotortium = "Robert Irelan <rirelan@gmail.com>";
   thall = "Niclas Thall <niclas.thall@gmail.com>";
   thammers = "Tobias Hammerschmidt <jawr@gmx.de>";

nixos/modules/virtualisation/docker.nix

@@ -126,14 +126,23 @@ in
         '';
       };
     };
+
+    package = mkOption {
+      default = pkgs.docker;
+      type = types.package;
+      example = pkgs.docker-edge;
+      description = ''
+        Docker package to be used in the module.
+      '';
+    };
   };
 
   ###### implementation
 
   config = mkIf cfg.enable (mkMerge [{
-      environment.systemPackages = [ pkgs.docker ];
+      environment.systemPackages = [ cfg.package ];
       users.extraGroups.docker.gid = config.ids.gids.docker;
-      systemd.packages = [ pkgs.docker ];
+      systemd.packages = [ cfg.package ];
 
       systemd.services.docker = {
         wantedBy = optional cfg.enableOnBoot "multi-user.target";
@@ -142,7 +151,7 @@ in
           ExecStart = [
             ""
             ''
-              ${pkgs.docker}/bin/dockerd \
+              ${cfg.package}/bin/dockerd \
                 --group=docker \
                 --host=fd:// \
                 --log-driver=${cfg.logDriver} \
@@ -180,7 +189,7 @@ in
         serviceConfig.Type = "oneshot";
 
         script = ''
-          ${pkgs.docker}/bin/docker system prune -f ${toString cfg.autoPrune.flags}
+          ${cfg.package}/bin/docker system prune -f ${toString cfg.autoPrune.flags}
         '';
 
         startAt = optional cfg.autoPrune.enable cfg.autoPrune.dates;

nixos/release-combined.nix

@@ -81,7 +81,10 @@ in rec {
         (all nixos.tests.boot.uefiUsb)
         (all nixos.tests.boot-stage1)
         nixos.tests.hibernate.x86_64-linux # i686 is flaky, see #23107
+        nixos.tests.docker.x86_64-linux
+        nixos.tests.docker-edge.x86_64-linux
         (all nixos.tests.ecryptfs)
+        (all nixos.tests.env)
         (all nixos.tests.ipv6)
         (all nixos.tests.i3wm)
         (all nixos.tests.keymap.azerty)
@@ -93,6 +96,7 @@ in rec {
         (all nixos.tests.plasma5)
         (all nixos.tests.kernel-latest)
         (all nixos.tests.kernel-lts)
+        (all nixos.tests.kernel-params)
         #(all nixos.tests.lightdm)
         (all nixos.tests.login)
         (all nixos.tests.misc)
@@ -115,8 +119,10 @@ in rec {
         (all nixos.tests.sddm.default)
         (all nixos.tests.simple)
         (all nixos.tests.slim)
+        (all nixos.tests.sysctl)
         (all nixos.tests.udisks2)
         (all nixos.tests.xfce)
+        (all nixos.tests.xmonad)
 
         nixpkgs.tarball
         (all allSupportedNixpkgs.emacs)

nixos/release.nix

@@ -234,12 +234,14 @@ in rec {
   tests.containers-hosts = callTest tests/containers-hosts.nix {};
   tests.containers-macvlans = callTest tests/containers-macvlans.nix {};
   tests.docker = hydraJob (import tests/docker.nix { system = "x86_64-linux"; });
+  tests.docker-edge = hydraJob (import tests/docker-edge.nix { system = "x86_64-linux"; });
   tests.dnscrypt-proxy = callTest tests/dnscrypt-proxy.nix { system = "x86_64-linux"; };
   tests.ecryptfs = callTest tests/ecryptfs.nix {};
   tests.etcd = hydraJob (import tests/etcd.nix { system = "x86_64-linux"; });
   tests.ec2-nixops = hydraJob (import tests/ec2.nix { system = "x86_64-linux"; }).boot-ec2-nixops;
   tests.ec2-config = hydraJob (import tests/ec2.nix { system = "x86_64-linux"; }).boot-ec2-config;
   tests.elk = callTest tests/elk.nix {};
+  tests.env = callTest tests/env.nix {};
   tests.ferm = callTest tests/ferm.nix {};
   tests.firefox = callTest tests/firefox.nix {};
   tests.firewall = callTest tests/firewall.nix {};
@@ -264,6 +266,7 @@ in rec {
   tests.kernel-copperhead = tests/kernel-copperhead.nix {};
   tests.kernel-latest = tests/kernel-latest.nix {};
   tests.kernel-lts = tests/kernel-lts.nix {};
+  tests.kernel-params = tests/kernel-params.nix {};
   tests.keystone = callTest tests/keystone.nix {};
   tests.kubernetes = hydraJob (import tests/kubernetes.nix { system = "x86_64-linux"; });
   tests.latestKernel.login = callTest tests/login.nix { latestKernel = true; };
@@ -309,12 +312,14 @@ in rec {
   tests.slim = callTest tests/slim.nix {};
   tests.smokeping = callTest tests/smokeping.nix {};
   tests.snapper = callTest tests/snapper.nix {};
+  tests.sysctl = callTest tests/sysctl.nix {};
   tests.taskserver = callTest tests/taskserver.nix {};
   tests.tomcat = callTest tests/tomcat.nix {};
   tests.udisks2 = callTest tests/udisks2.nix {};
   tests.virtualbox = callSubTests tests/virtualbox.nix { system = "x86_64-linux"; };
   tests.wordpress = callTest tests/wordpress.nix {};
   tests.xfce = callTest tests/xfce.nix {};
+  tests.xmonad = callTest tests/xmonad.nix {};
 
 
   /* Build a bunch of typical closures so that Hydra can keep track of

nixos/tests/docker-edge.nix

@@ -0,0 +1,47 @@
+# This test runs docker and checks if simple container starts
+
+import ./make-test.nix ({ pkgs, ...} : {
+  name = "docker";
+  meta = with pkgs.stdenv.lib.maintainers; {
+    maintainers = [ nequissimus offline ];
+  };
+
+  nodes = {
+    docker =
+      { config, pkgs, ... }:
+        {
+          virtualisation.docker.enable = true;
+          virtualisation.docker.package = pkgs.docker-edge;
+
+          users.users = {
+            noprivs = {
+              isNormalUser = true;
+              description = "Can't access the docker daemon";
+              password = "foobar";
+            };
+
+            hasprivs = {
+              isNormalUser = true;
+              description = "Can access the docker daemon";
+              password = "foobar";
+              extraGroups = [ "docker" ];
+            };
+          };
+        };
+    };
+
+  testScript = ''
+    startAll;
+
+    $docker->waitForUnit("sockets.target");
+    $docker->succeed("tar cv --files-from /dev/null | docker import - scratchimg");
+    $docker->succeed("docker run -d --name=sleeping -v /nix/store:/nix/store -v /run/current-system/sw/bin:/bin scratchimg /bin/sleep 10");
+    $docker->succeed("docker ps | grep sleeping");
+    $docker->succeed("sudo -u hasprivs docker ps");
+    $docker->fail("sudo -u noprivs docker ps");
+    $docker->succeed("docker stop sleeping");
+
+    # Must match version twice to ensure client and server versions are correct
+    $docker->succeed('[ $(docker version | grep ${pkgs.docker-edge.version} | wc -l) = "2" ]');
+  '';
+})

nixos/tests/docker.nix

@@ -3,7 +3,7 @@
 import ./make-test.nix ({ pkgs, ...} : {
   name = "docker";
   meta = with pkgs.stdenv.lib.maintainers; {
-    maintainers = [ offline ];
+    maintainers = [ nequissimus offline ];
   };
 
   nodes = {
@@ -11,6 +11,7 @@ import ./make-test.nix ({ pkgs, ...} : {
       { config, pkgs, ... }:
         {
           virtualisation.docker.enable = true;
+          virtualisation.docker.package = pkgs.docker;
 
           users.users = {
             noprivs = {
@@ -39,5 +40,8 @@ import ./make-test.nix ({ pkgs, ...} : {
     $docker->succeed("sudo -u hasprivs docker ps");
     $docker->fail("sudo -u noprivs docker ps");
     $docker->succeed("docker stop sleeping");
+
+    # Must match version twice to ensure client and server versions are correct
+    $docker->succeed('[ $(docker version | grep ${pkgs.docker.version} | wc -l) = "2" ]');
   '';
 })

nixos/tests/env.nix

@@ -0,0 +1,35 @@
+import ./make-test.nix ({ pkgs, ...} : {
+  name = "environment";
+  meta = with pkgs.stdenv.lib.maintainers; {
+    maintainers = [ nequissimus ];
+  };
+
+  machine = { config, lib, pkgs, ... }:
+    {
+      boot.kernelPackages = pkgs.linuxPackages;
+      environment.etc."plainFile".text = ''
+        Hello World
+      '';
+      environment.etc."folder/with/file".text = ''
+        Foo Bar!
+      '';
+
+      environment.sessionVariables = {
+        TERMINFO_DIRS = "/run/current-system/sw/share/terminfo";
+        NIXCON = "awesome";
+      };
+    };
+
+  testScript =
+    ''
+      $machine->succeed('[ -L "/etc/plainFile" ]');
+      $machine->succeed('cat "/etc/plainFile" | grep "Hello World"');
+      $machine->succeed('[ -d "/etc/folder" ]');
+      $machine->succeed('[ -d "/etc/folder/with" ]');
+      $machine->succeed('[ -L "/etc/folder/with/file" ]');
+      $machine->succeed('cat "/etc/plainFile" | grep "Hello World"');
+
+      $machine->succeed('echo ''${TERMINFO_DIRS} | grep "/run/current-system/sw/share/terminfo"');
+      $machine->succeed('echo ''${NIXCON} | grep "awesome"');
+    '';
+})

nixos/tests/kernel-params.nix

@@ -0,0 +1,24 @@
+import ./make-test.nix ({ pkgs, ...} : {
+  name = "kernel-params";
+  meta = with pkgs.stdenv.lib.maintainers; {
+    maintainers = [ nequissimus ];
+  };
+
+  machine = { config, lib, pkgs, ... }:
+    {
+      boot.kernelPackages = pkgs.linuxPackages;
+      boot.kernelParams = [
+        "nohibernate"
+        "page_poison=1"
+        "vsyscall=none"
+      ];
+    };
+
+  testScript =
+    ''
+      $machine->fail("cat /proc/cmdline | grep page_poison=0");
+      $machine->succeed("cat /proc/cmdline | grep nohibernate");
+      $machine->succeed("cat /proc/cmdline | grep page_poison=1");
+      $machine->succeed("cat /proc/cmdline | grep vsyscall=none");
+    '';
+})

nixos/tests/sysctl.nix

@@ -0,0 +1,25 @@
+import ./make-test.nix ({ pkgs, ...} : {
+  name = "sysctl";
+  meta = with pkgs.stdenv.lib.maintainers; {
+    maintainers = [ nequissimus ];
+  };
+
+  machine = { config, lib, pkgs, ... }:
+    {
+      boot.kernelPackages = pkgs.linuxPackages;
+      boot.kernel.sysctl = {
+        "kernel.dmesg_restrict" = true; # Restrict dmesg access
+        "net.core.bpf_jit_enable" = false; # Turn off bpf JIT
+        "user.max_user_namespaces" = 0; # Disable user namespaces
+        "vm.swappiness" = 2; # Low swap usage
+      };
+    };
+
+  testScript =
+    ''
+      $machine->succeed("sysctl kernel.dmesg_restrict | grep 'kernel.dmesg_restrict = 1'");
+      $machine->succeed("sysctl net.core.bpf_jit_enable | grep 'net.core.bpf_jit_enable = 0'");
+      $machine->succeed("sysctl user.max_user_namespaces | grep 'user.max_user_namespaces = 0'");
+      $machine->succeed("sysctl vm.swappiness | grep 'vm.swappiness = 2'");
+    '';
+})

nixos/tests/xmonad.nix

@@ -0,0 +1,28 @@
+import ./make-test.nix ({ pkgs, ...} : {
+  name = "xmonad";
+  meta = with pkgs.stdenv.lib.maintainers; {
+    maintainers = [ nequissimus ];
+  };
+
+  machine = { lib, pkgs, ... }: {
+    imports = [ ./common/x11.nix ./common/user-account.nix ];
+    services.xserver.displayManager.auto.user = "alice";
+    services.xserver.windowManager.default = lib.mkForce "xmonad";
+    services.xserver.windowManager.xmonad = {
+      enable = true;
+      enableContribAndExtras = true;
+      extraPackages = with pkgs.haskellPackages; haskellPackages: [ xmobar ];
+    };
+  };
+
+  testScript = { nodes, ... }: ''
+    $machine->waitForX;
+    $machine->waitForFile("/home/alice/.Xauthority");
+    $machine->succeed("xauth merge ~alice/.Xauthority");
+    $machine->sleep(3);
+    $machine->sendKeys("alt-shift-ret");
+    $machine->waitForWindow(qr/machine.*alice/);
+    $machine->sleep(1);
+    $machine->screenshot("terminal");
+  '';
+})

pkgs/applications/misc/toot/default.nix

@@ -1,19 +1,25 @@
 { stdenv, fetchFromGitHub, pythonPackages }:
 
 pythonPackages.buildPythonApplication rec {
-  version = "0.8.0";
+  version = "0.13.0";
   name    = "toot-${version}";
 
   src = fetchFromGitHub {
     owner  = "ihabunek";
     repo   = "toot";
     rev    = "${version}";
-    sha256 = "1y1jz4f53njq94zab0icf7jhd4jp10ywm508l4lw6spb69wr7rdy";
+    sha256 = "0gbsq43qv5qg4avx7czs57k40m8lzh8f1z5yizqqc7r02p2sacnc";
   };
 
+  checkInputs = with pythonPackages; [ pytest ];
+
   propagatedBuildInputs = with pythonPackages;
     [ requests beautifulsoup4 future ];
 
+  checkPhase = ''
+    py.test
+  '';
+
   meta = with stdenv.lib; {
     description = "Mastodon CLI interface";
     homepage    = "https://github.com/ihabunek/toot";

pkgs/applications/networking/syncthing/default.nix

@@ -1,14 +1,14 @@
 { stdenv, lib, fetchFromGitHub, go, procps, removeReferencesTo }:
 
 stdenv.mkDerivation rec {
-  version = "0.14.36";
+  version = "0.14.37";
   name = "syncthing-${version}";
 
   src = fetchFromGitHub {
     owner  = "syncthing";
     repo   = "syncthing";
     rev    = "v${version}";
-    sha256 = "1l4s74qlabwfkpi9lmm588ym0myavbs06a5gpp9nihzrsal18727";
+    sha256 = "0mk09m5wc6g7w65cf86rrvzb2gfzbg4jrkwpsabn732iyhkkaj4z";
   };
 
   buildInputs = [ go removeReferencesTo ];

pkgs/applications/science/electronics/adms/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, fetchFromGitHub, libtool, autoreconfHook, flex, bison, gperf,
+  libxml2, perl, perlPackages, gd }:
+
+stdenv.mkDerivation rec {
+  version = "2.3.6";
+  name = "adms-${version}";
+
+  src = fetchFromGitHub {
+    owner = "Qucs";
+    repo = "adms";
+    rev = "release-${version}";
+    sha256 = "1pcwq5khzdq4x33lid9hq967gv78dr5i4f2sk8m8rwkfqb9vdzrg";
+  };
+
+  buildInputs = [ autoreconfHook flex bison gperf libxml2 perl gd perlPackages.XMLLibXML ];
+  configureFlags = [ "--enable-maintainer-mode" ];
+
+  meta = {
+    description = "automatic device model synthesizer";
+    homepage = https://github.com/Qucs/adms;
+    license = stdenv.lib.licenses.gpl3;
+    maintainers = with stdenv.lib.maintainers; [disassembler];
+    platforms = with stdenv.lib.platforms; linux;
+  };
+}

pkgs/applications/science/electronics/qucs/cmakelists.patch

@@ -0,0 +1,34 @@
+diff --git i/qucs-core/CMakeLists.txt w/qucs-core/CMakeLists.txt
+index 2dbbd41..d174b50 100644
+--- i/qucs-core/CMakeLists.txt
++++ w/qucs-core/CMakeLists.txt
+@@ -158,26 +158,9 @@ ENDIF()
+ 
+ #
+ # Need Bison
+-#
+-# This is a HACK to get arround a PATH issue with Qt Creator on OSX.
+-# It seams impossible to pass a custom PATH to Qt Creator on OSX, ie, cannot prepend `/usr/local/bin/` for intance.
+-# The FIND_PACKAGE fails. For now we provide a fallback with a custom FIND_PROGRAM. The variable BISON_DIR is also available.
+-IF(WIN32)
+-  FIND_PACKAGE(BISON 2.4 REQUIRED)
+-  IF(BISON_FOUND)
+-    #MESSAGE(STATUS "Found bison: ${BISON_EXECUTABLE} / Version: ${BISON_VERSION}" )
+-  ENDIF()
+-ELSE()  # Linux, OSX
+-  # use -DBISON_DIR=/path/ to provide the path to bison
+-  FIND_PROGRAM( BISON_EXECUTABLE bison
+-    PATHS /usr/local/bin/ /opt/local/bin/ /usr/bin ${BISON_DIR}
+-    DOC "bison path"
+-    NO_DEFAULT_PATH )
+-  IF(BISON_EXECUTABLE )
+-    MESSAGE(STATUS "Found bison: " ${BISON_EXECUTABLE})
+-  ELSE()
+-	  MESSAGE(FATAL_ERROR "Unable to find bison. Try to provide -DBISON_DIR=[path]")
+-  ENDIF()
++FIND_PACKAGE(BISON 2.4 REQUIRED)
++IF(BISON_FOUND)
++  #MESSAGE(STATUS "Found bison: ${BISON_EXECUTABLE} / Version: ${BISON_VERSION}" )
+ ENDIF()
+ 
+ #

pkgs/applications/science/electronics/qucs/default.nix

@@ -1,16 +1,23 @@
-{stdenv, fetchurl, flex, bison, qt4, libX11 }:
+{stdenv, fetchFromGitHub, flex, bison, qt4, libX11, cmake, gperf, adms }:
 
 stdenv.mkDerivation rec {
-  name = "qucs-0.0.18";
+  version = "0.0.19";
+  name = "qucs-${version}";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/qucs/${name}.tar.gz";
-    sha256 = "3609a18b57485dc9f19886ac6694667f3251702175bd1cbbbea37981b2c482a7";
+  src = fetchFromGitHub {
+    owner = "Qucs";
+    repo = "qucs";
+    rev = "qucs-${version}";
+    sha256 = "106h3kjyg7c0hkmzkin7h8fcl32n60835121b2qqih8ixi6r5id6";
   };
 
   QTDIR=qt4;
 
-  buildInputs = [ flex bison qt4 libX11 ];
+  patches = [
+    ./cmakelists.patch
+  ];
+
+  buildInputs = [ flex bison qt4 libX11 cmake gperf adms ];
 
   meta = {
     description = "Integrated circuit simulator";

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

@@ -2,10 +2,10 @@
 # - The csdp program used for the Micromega tactic is statically referenced.
 #   However, coq can build without csdp by setting it to null.
 #   In this case some Micromega tactics will search the user's path for the csdp program and will fail if it is not found.
-# - The patch-level version can be specified through the `version` argument to
-#   the derivation; it defaults to the greatest.
+# - The exact version can be specified through the `version` argument to
+#   the derivation; it defaults to the latest stable version.
 
-{ stdenv, fetchurl, writeText, pkgconfig
+{ stdenv, fetchFromGitHub, writeText, pkgconfig
 , ocamlPackages, ncurses
 , buildIde ? true
 , csdp ? null
@@ -14,11 +14,12 @@
 
 let
   sha256 = {
-   "8.5pl1"	= "1w2xvm6w16khfn63bp95s25hnkn2ny3w0yqg3lq63gp11aqpbyjb";
-   "8.5pl2"	= "0wyywia0darak2zmc5v0ra9rn0b9whwdfiahralm8v5za499s8w3";
-   "8.5pl3"	= "0fyk2a4fpifibq8y8jhx1891k55qnsnlygglch64sva0bph94nrh";
-   "8.6"	= "1pw1xvy1657l1k69wrb911iqqflzhhp8wwsjvihbgc72r3skqg3f";
-   "8.6.1"      = "17cg2c40y9lskkiqfhngavp8yw3shpqgkpihh30xx0rlhn9amy1j";
+   "8.5pl1"    = "1976ki5xjg2r907xj9p7gs0kpdinywbwcqlgxqw75dgp0hkgi00n";
+   "8.5pl2"    = "109rrcrx7mz0fj7725kjjghfg5ydwb24hjsa5hspa27b4caah7rh";
+   "8.5pl3"    = "15c3rdk59nifzihsp97z4vjxis5xmsnrvpb86qiazj143z2fmdgw";
+   "8.6"       = "148mb48zpdax56c0blfi7v67lx014lnmrvxxasi28hsibyz2lvg4";
+   "8.6.1"     = "0llrxcxwy5j87vbbjnisw42rfw1n1pm5602ssx64xaxx3k176g6l";
+   "8.7+beta1" = "006rn5896pf39p4z9c6d4xj4zm80j4b67v5gwcixd63msrjqkmxp";
   }."${version}";
   coq-version = builtins.substring 0 3 version;
   camlp5 = ocamlPackages.camlp5_strict;
@@ -81,8 +82,10 @@ self = stdenv.mkDerivation {
     '';
   };
 
-  src = fetchurl {
-    url = "http://coq.inria.fr/distrib/V${version}/files/coq-${version}.tar.gz";
+  src = fetchFromGitHub {
+    owner = "coq";
+    repo = "coq";
+    rev = "V${version}";
     inherit sha256;
   };
 

pkgs/applications/virtualization/docker/default.nix

@@ -177,13 +177,13 @@ rec {
   # https://github.com/docker/docker-ce/blob/v${version}/components/engine/hack/dockerfile/binaries-commits
 
   docker_17_06 = dockerGen rec {
-    version = "17.06.1-ce";
-    rev = "874a7374f31c77aca693d025101b2de1b20b96c2"; # git commit
-    sha256 = "08xhww2rhpyj73zgh5maycs85zpc0sm3ak8yyyd92dwgncmyi2im";
-    runcRev = "2d41c047c83e09a6d61d464906feb2a2f3c52aa4";
-    runcSha256 = "0v5iv29ck6lkxvxh7a56gfrlgfs0bjvjhrq3p6qqv9qjzv825byq";
-    containerdRev = "3addd840653146c90a254301d6c3a663c7fd6429";
-    containerdSha256 = "0as4s5wd57pdh1cyavkccpgs46kvlhr41v07qrv0phzffdhq3d5j";
+    version = "17.06.2-ce";
+    rev = "cec0b72a9940e047e945a09e1febd781e88366d6"; # git commit
+    sha256 = "1scqx28vzh72ziq00lbx92vsb896mj974j8f0zg11y6qc5n5jx3l";
+    runcRev = "810190ceaa507aa2727d7ae6f4790c76ec150bd2";
+    runcSha256 = "0f1x1z262qg579qb1w21axj3mibq4fbff3gamliw49sdqqnb7vk3";
+    containerdRev = "6e23458c129b551d5c9871e5174f6b1b7f6d1170";
+    containerdSha256 = "12kzc5z1nhxdbizzr494ywilbs6rdv39v5ql7lmfzwh350gwlg93";
     tiniRev = "949e6facb77383876aeff8a6944dde66b3089574";
     tiniSha256 = "0zj4kdis1vvc6dwn4gplqna0bs7v6d1y2zc8v80s3zi018inhznw";
   };

pkgs/development/libraries/protobuf/3.3.nix

@@ -0,0 +1,6 @@
+{ callPackage, lib, ... }:
+
+lib.overrideDerivation (callPackage ./generic-v3.nix {
+  version = "3.3.0";
+  sha256 = "1258yz9flyyaswh3izv227kwnhwcxn4nwavdz9iznqmh24qmi59w";
+}) (attrs: { NIX_CFLAGS_COMPILE = "-Wno-error"; })

pkgs/development/libraries/science/math/cudnn/8.0-6.0/default.nix

@@ -0,0 +1,40 @@
+{ stdenv
+, requireFile
+, cudatoolkit
+, fetchurl
+}:
+
+stdenv.mkDerivation rec {
+  version = "6.0";
+  cudatoolkit_version = "8.0";
+
+  name = "cudatoolkit-${cudatoolkit_version}-cudnn-${version}";
+
+  src = fetchurl {
+    url = "http://developer.download.nvidia.com/compute/redist/cudnn/v6.0/cudnn-8.0-linux-x64-v6.0.tgz";
+    sha256 = "173zpgrk55ri8if7s5yngsc89ajd6hz4pss4cdxlv6lcyh5122cv";
+  };
+
+  installPhase = ''
+    function fixRunPath {
+      p=$(patchelf --print-rpath $1)
+      patchelf --set-rpath "$p:${stdenv.lib.makeLibraryPath [ stdenv.cc.cc ]}" $1
+    }
+    fixRunPath lib64/libcudnn.so
+
+    mkdir -p $out
+    cp -a include $out/include
+    cp -a lib64 $out/lib64
+  '';
+
+  propagatedBuildInputs = [
+    cudatoolkit
+  ];
+
+  meta = with stdenv.lib; {
+    description = "NVIDIA CUDA Deep Neural Network library (cuDNN)";
+    homepage = https://developer.nvidia.com/cudnn;
+    license = stdenv.lib.licenses.unfree;
+    maintainers = with maintainers; [ jpbernardy ];
+  };
+}

pkgs/development/libraries/ucl/default.nix

@@ -1,4 +1,4 @@
-{stdenv, fetchurl}:
+{ stdenv, fetchurl }:
 
 stdenv.mkDerivation {
   name = "ucl-1.03";
@@ -8,7 +8,7 @@ stdenv.mkDerivation {
   };
 
   # needed to successfully compile with gcc 6
-  NIX_CFLAGS_COMPILE = "-std=c90 -fPIC";
+  NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.cc.isGNU "-std=c90";
 
   meta = {
     homepage = http://www.oberhumer.com/opensource/ucl/;

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

@@ -0,0 +1,24 @@
+{ lib, buildPythonPackage, fetchPypi, isPy33, pythonOlder,
+  asyncio
+}:
+
+buildPythonPackage rec {
+  pname = "aioamqp";
+  name = "${pname}-${version}";
+  version = "0.10.0";
+
+  meta = {
+    homepage = https://github.com/polyconseil/aioamqp;
+    description = "AMQP implementation using asyncio";
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0132921yy31ijb8w439zcz1gla4hiws4hx8zf6la4hjr01nsy666";
+  };
+
+  buildInputs = lib.optionals isPy33 [ asyncio ];
+
+  disabled = pythonOlder "3.3";
+}

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

@@ -0,0 +1,37 @@
+{ lib, buildPythonPackage, fetchPypi,
+  pytest, requests, requests_oauthlib, six
+}:
+
+buildPythonPackage rec {
+  pname = "asana";
+  version = "0.6.2";
+  name = "${pname}-${version}";
+
+  meta = {
+    description = "Python client library for Asana";
+    homepage = https://github.com/asana/python-asana;
+    license = lib.licenses.mit;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0skai72392n3i1c4bl3hn2kh5lj990qsbasdwkbjdcy6vq57jggf";
+  };
+
+  buildInputs = [ pytest ];
+  propagatedBuildInputs = [ requests requests_oauthlib six ];
+
+  patchPhase = ''
+    echo > requirements.txt
+    sed -i "s/requests~=2.9.1/requests >=2.9.1/" setup.py
+    sed -i "s/requests_oauthlib~=0.6.1/requests_oauthlib >=0.6.1/" setup.py
+  '';
+
+  # ERROR: file not found: tests
+  doCheck = false; 
+
+  checkPhase = ''
+    py.test tests
+  '';
+
+}

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

@@ -2,9 +2,7 @@
 , fetchPypi
 , buildPythonPackage
 , numpy
-, cython
-, h5py
-, scipy }:
+, pytest }:
 
 buildPythonPackage rec {
   
@@ -17,7 +15,8 @@ buildPythonPackage rec {
     inherit pname version;
     sha256 = "25e0881a392a2e03b4a705cf9592f01894d23f64797323b21387efa8ea9ec03e";
   };
-  propagatedBuildInputs = [ numpy cython h5py scipy ];
+
+  propagatedBuildInputs = [ pytest numpy ]; # yes it really has pytest in install_requires
 
 
   meta = {

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

@@ -0,0 +1,33 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, setuptools_scm
+# , backports
+, python
+}:
+
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "backports.weakref";
+  version = "1.0rc1";
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "14i8m3lspykdfpzf50grij3z286j9q8f32f2bnwdicv659qvy4w8";
+  };
+
+  buildInputs = [ setuptools_scm ];
+#   checkInputs = [ backports ];
+
+  # Requires backports package
+  doCheck = false;
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover tests
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Backports of new features in Python’s weakref module";
+    license = licenses.psfl;
+    maintainers = with maintainers; [ jpbernardy ];
+  };
+}

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

@@ -0,0 +1,45 @@
+{ stdenv, fetchPypi
+, buildPythonApplication, python, pythonAtLeast
+, mock, nose, pyhamcrest
+, glibcLocales, parse, parse-type, six
+}:
+buildPythonApplication rec {
+  pname = "behave";
+  version = "1.2.5";
+  name = "${pname}-${version}";
+
+  disabled = pythonAtLeast "3.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "81b731ac5187e31e4aad2594944fa914943683a9818320846d037c5ebd6d5d0b";
+  };
+
+  checkInputs = [ mock nose pyhamcrest ];
+  buildInputs = [ glibcLocales ];
+  propagatedBuildInputs = [ parse parse-type six ];
+
+  postPatch = ''
+    patchShebangs bin
+  '';
+
+  doCheck = true;
+
+  checkPhase = ''
+    export LANG="en_US.UTF-8"
+    export LC_ALL="en_US.UTF-8"
+
+    nosetests -x
+
+    ${python.interpreter} bin/behave -f progress3 --stop --tags='~@xfail' features/
+    ${python.interpreter} bin/behave -f progress3 --stop --tags='~@xfail' tools/test-features/
+    ${python.interpreter} bin/behave -f progress3 --stop --tags='~@xfail' issue.features/
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/behave/behave;
+    description = "behaviour-driven development, Python style";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ alunduil ];
+  };
+}

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

@@ -2,12 +2,15 @@
 , lib
 , fetchPypi
 , mock
-, pytest_27
+, pytest
+, pytestrunner
 , sh
 , coverage
 , docopt
 , requests
+, urllib3
 , git
+, isPy3k
 }:
 
 buildPythonPackage rec {
@@ -21,13 +24,17 @@ buildPythonPackage rec {
     sha256 = "510682001517bcca1def9f6252df6ce730fcb9831c62d9fff7c7d55b6fdabdf3";
   };
 
-  buildInputs = [
+  checkInputs = [
     mock
     sh
-    pytest_27
+    pytest
     git
   ];
 
+  buildInputs = [
+    pytestrunner
+  ];
+
   # FIXME: tests requires .git directory to be present
   doCheck = false;
 
@@ -39,7 +46,7 @@ buildPythonPackage rec {
     coverage
     docopt
     requests
-  ];
+  ] ++ lib.optional (!isPy3k) urllib3;
 
   meta = {
     description = "Show coverage stats online via coveralls.io";

pkgs/development/python-modules/diff-match-patch/default.nix

@@ -0,0 +1,18 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "diff-match-patch";
+  name = "${pname}-${version}";
+  version = "20121119";
+
+  meta = {
+    homepage = https://code.google.com/p/google-diff-match-patch/;
+    description = "Diff, Match and Patch libraries for Plain Text";
+    license = lib.licenses.asl20;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0k1f3v8nbidcmmrk65m7h8v41jqi37653za9fcs96y7jzc8mdflx";
+  };
+}

pkgs/development/python-modules/django-ipware/default.nix

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchPypi, django }:
+
+buildPythonPackage rec {
+  pname = "django-ipware";
+  name = "${pname}-${version}";
+  version = "1.1.6";
+
+  meta = {
+    description = "A Django application to retrieve user's IP address";
+    homepage = https://github.com/un33k/django-ipware;
+    license = lib.licenses.mit;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "00zah4g2h93nbsijz556j97v9qkn9sxcia1a2wrwdwnav2fhzack";
+  };
+
+  propagatedBuildInputs = [ django ];
+
+  # django.core.exceptions.ImproperlyConfigured: Requested setting IPWARE_TRUSTED_PROXY_LIST, but settings are not configured. You must either define the environment variable DJANGO_SETTINGS_MODULE or call settings.configure() before accessing settings.
+  doCheck = false;
+}

pkgs/development/python-modules/django-jinja2/default.nix

@@ -0,0 +1,29 @@
+{ lib, buildPythonPackage, fetchPypi,
+  django, jinja2, pytz, tox
+ }:
+
+buildPythonPackage rec {
+  pname = "django-jinja";
+  name = "${pname}-${version}";
+  version = "2.2.2";
+
+  meta = {
+    description = "Simple and nonobstructive jinja2 integration with Django";
+    homepage = https://github.com/niwinz/django-jinja;
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "099b99iprkvlsndrjmw4v3i3i60i9gm1aq5r88z15r7vgmv6sigj";
+  };
+
+  buildInputs = [ django pytz tox ];
+  propagatedBuildInputs = [ django jinja2 ];
+
+  # python installed: The directory '/homeless-shelter/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.,appdirs==1.4.3,Django==1.11.1,django-jinja==2.2.2,Jinja2==2.9.6,MarkupSafe==1.0,packaging==16.8,pyparsing==2.2.0,pytz==2017.2,six==1.10.0
+  doCheck = false;
+  checkPhase = ''
+    tox
+  '';
+}

pkgs/development/python-modules/django-pglocks/default.nix

@@ -0,0 +1,24 @@
+{ lib, buildPythonPackage, fetchPypi, django }:
+
+buildPythonPackage rec {
+  pname = "django-pglocks";
+  name = "${pname}-${version}";
+  version = "1.0.2";
+
+  meta = {
+    description = "PostgreSQL locking context managers and functions for Django.";
+    homepage = https://github.com/Xof/django-pglocks;
+    license = lib.licenses.mit;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ks4k0bk4457wfl3xgzr4v7xb0lxmnkhxwhlp0bbnmzipdafw1cl";
+  };
+
+  buildInputs = [ django ];
+  propagatedBuildInputs = [ django ];
+
+  # tests need a postgres database
+  doCheck = false;
+}

pkgs/development/python-modules/django-picklefield/default.nix

@@ -0,0 +1,18 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "django-picklefield";
+  name = "${pname}-${version}";
+  version = "0.3.2";
+
+  meta = {
+    description = "A pickled object field for Django";
+    homepage = https://github.com/gintas/django-picklefield;
+    license = lib.licenses.mit;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1qlsbp3798ii68ny9zlz2ppkna00jf7i4hmjal3p8433gi18md7s";
+  };
+}

pkgs/development/python-modules/django-sampledatahelper/default.nix

@@ -0,0 +1,31 @@
+{ lib, buildPythonPackage, fetchPypi,
+  django, nose, pillow, sampledata, six, versiontools
+}:
+
+buildPythonPackage rec {
+  pname = "django-sampledatahelper";
+  name = "${pname}-${version}";
+  version = "0.4.1";
+
+  meta = {
+    description = "Helper class for generate sample data for django apps development";
+    homepage = https://github.com/kaleidos/django-sampledatahelper;
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1795zg73lajcsfyd8i8cprb2v93d4csifjnld6bfnya90ncsbl4n";
+  };
+
+  buildInputs = [ django nose pillow sampledata six versiontools ];
+  propagatedBuildInputs = [ django sampledata ];
+
+  # HACK To prevent collision with pythonPackages.sampledata
+  preBuild = ''
+    rm tests/*
+  '';
+
+  # ERROR: test_image_from_directory (tests.tests.TestImageHelpers)
+  doCheck = false;
+}

pkgs/development/python-modules/django-sites/default.nix

@@ -0,0 +1,26 @@
+{ lib, buildPythonPackage, fetchPypi, django }:
+
+buildPythonPackage rec {
+  pname = "django-sites";
+  name = "${pname}-${version}";
+  version = "0.9";
+
+  meta = {
+    description = ''
+      Alternative implementation of django "sites" framework
+      based on settings instead of models.
+    '';
+    homepage = https://github.com/niwinz/django-sites;
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "05nrydk4a5a99qrxjrcnacs8nbbq5pfjikdpj4w9yn5yfayp057s";
+  };
+
+  propagatedBuildInputs = [ django ];
+
+  # django.core.exceptions.ImproperlyConfigured: Requested settings, but settings are not configured. You must either define the environment variable DJANGO_SETTINGS_MODULE or call settings.configure() before accessing settings.
+  doCheck = false;
+}

pkgs/development/python-modules/django-sr/default.nix

@@ -0,0 +1,21 @@
+{ lib, buildPythonPackage, fetchPypi, django, nose }:
+
+buildPythonPackage rec {
+  pname = "django-sr";
+  name = "${pname}-${version}";
+  version = "0.0.4";
+
+  meta = {
+    description = "Django settings resolver";
+    homepage = https://github.com/jespino/django-sr;
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0d3yqppi1q3crcn9nxx58wzm4yw61d5m7435g6rb9wcamr9bi1im";
+  };
+
+  buildInputs = [ django nose ];
+  propagatedBuildInputs = [ django ];
+}

pkgs/development/python-modules/django/1_11.nix

@@ -5,13 +5,13 @@
 buildPythonPackage rec {
   pname = "Django";
   name = "${pname}-${version}";
-  version = "1.11.4";
+  version = "1.11.5";
 
   disabled = pythonOlder "2.7";
 
   src = fetchurl {
     url = "http://www.djangoproject.com/m/releases/1.11/${name}.tar.gz";
-    sha256 = "1ckvq2sdlgpy2sqy6fwl84ms9dggvdbys9x76qapm2d9vmknxs5b";
+    sha256 = "0a9bk1a0n0264lcr67fmwzqyhkhy6bqdzkxsj9a8dpyzca0qfdhq";
   };
 
   patches = [

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

@@ -0,0 +1,25 @@
+{ lib, buildPythonPackage, fetchPypi,
+  celery, django, psycopg2
+}:
+
+buildPythonPackage rec {
+  pname = "djmail";
+  name = "${pname}-${version}";
+  version = "1.0.1";
+
+  meta = {
+    description = "Simple, powerfull and nonobstructive django email middleware.";
+    homepage = https://github.com/bameda/djmail;
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1827i9qcn1ki09i5pg0lmar7cxjv18avh76x1n20947p1cimf3rp";
+  };
+
+  propagatedBuildInputs = [ celery django psycopg2 ];
+
+  # django.core.exceptions.ImproperlyConfigured: Requested setting DEFAULT_INDEX_TABLESPACE, but settings are not configured. You must either define the environment variable DJANGO_SETTINGS_MODULE or call settings.configure() before accessing settings.
+  doCheck = false;
+}

pkgs/development/python-modules/easy-thumbnails/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi,
+  django, pillow
+}:
+
+buildPythonPackage rec {
+  pname = "easy-thumbnails";
+  name = "${pname}-${version}";
+  version = "2.4.1";
+
+  meta = {
+    description = "Easy thumbnails for Django";
+    homepage = https://github.com/SmileyChris/easy-thumbnails;
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0w228b6hx8k4r15v7z62hyg99qp6xp4mdkgqs1ah64fyqxp1riaw";
+  };
+
+  propagatedBuildInputs = [ django pillow ];
+}

pkgs/development/python-modules/flask-mail/default.nix

@@ -0,0 +1,25 @@
+{ lib, buildPythonPackage, fetchPypi,
+  blinker, flask, mock, nose, speaklater
+}:
+
+buildPythonPackage rec {
+  pname = "Flask-Mail";
+  name = "${pname}-${version}";
+  version = "0.9.1";
+
+  meta = {
+    description = "Flask-Mail is a Flask extension providing simple email sending capabilities.";
+    homepage = "https://pypi.python.org/pypi/Flask-Mail";
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0hazjc351s3gfbhk975j8k65cg4gf31yq404yfy0gx0bjjdfpr92";
+  };
+
+  propagatedBuildInputs = [ blinker flask ];
+  buildInputs = [ blinker mock nose speaklater ];
+
+  doCheck = false;
+}

pkgs/development/python-modules/flask-marshmallow/default.nix

@@ -0,0 +1,25 @@
+{ lib, buildPythonPackage, fetchPypi,
+  flask, six, marshmallow
+}:
+
+buildPythonPackage rec {
+  pname = "flask-marshmallow";
+  name = "${pname}-${version}";
+  version = "0.8.0";
+
+  meta = {
+    homepage = "https://github.com/marshmallow-code/flask-marshmallow";
+    description = "Flask + marshmallow for beautiful APIs";
+    license = lib.licenses.mit;
+  }; 
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1fa6xgxrn9bbc2pazbg46iw3ykvpcwib5b5s46qn59ndwj77lifi";
+  };
+
+  propagatedBuildInputs = [ flask marshmallow ];
+  buildInputs = [ six ];
+
+  doCheck = false;
+}

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

@@ -1,5 +1,5 @@
 { stdenv, buildPythonPackage, fetchPypi
-, itsdangerous, click, werkzeug, jinja2 }:
+, itsdangerous, click, werkzeug, jinja2, pytest }:
 
 buildPythonPackage rec {
   name = "${pname}-${version}";
@@ -11,8 +11,16 @@ buildPythonPackage rec {
     sha256 = "1hfs2jr2m5lr51xd4gblb28rncd0xrpycz6c07cyqsbv4dhl9x29";
   };
 
+  checkInputs = [ pytest ];
   propagatedBuildInputs = [ itsdangerous click werkzeug jinja2 ];
 
+  checkPhase = ''
+    py.test
+  '';
+
+  # Tests require extra dependencies
+  doCheck = false;
+
   meta = with stdenv.lib; {
     homepage = http://flask.pocoo.org/;
     description = "A microframework based on Werkzeug, Jinja 2, and good intentions";

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

@@ -0,0 +1,21 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "fn";
+  name = "${pname}-${version}";
+  version = "0.4.3";
+
+  meta = {
+    description = ''
+      Functional programming in Python: implementation of missing
+      features to enjoy FP
+    '';
+    homepage = https://github.com/kachayev/fn.py;
+    license = lib.licenses.asl20;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1nmsjmn8jb4gp22ksx0j0hhdf4y0zm8rjykyy2i6flzimg6q1kgq";
+  };
+}

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

@@ -5,6 +5,7 @@
 , wcwidth
 , nose
 , python
+, isPy3k
 }:
 buildPythonPackage rec {
   name = "${pname}-${version}";
@@ -18,14 +19,21 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ html5lib wcwidth];
 
-  buildInputs = [
+  checkInputs = [
     nose
   ];
 
   checkPhase = ''
-    nosetests -v
+    nosetests -v tests
   '';
 
+  # Several tests fail with
+  # FileNotFoundError: [Errno 2] No such file or directory: 'ftfy'
+  doCheck = false;
+
+  # "this version of ftfy is no longer written for Python 2"
+  disabled = !isPy3k;
+
   meta = with stdenv.lib; {
     description = "Given Unicode text, make its representation consistent and possibly less broken.";
     homepage = https://github.com/LuminosoInsight/python-ftfy/tree/master/tests;

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

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, buildPythonPackage, pycurl }:
+{ stdenv, fetchurl, buildPythonPackage, pycurl, isPy3k }:
 
 buildPythonPackage rec {
   pname = "koji";
@@ -7,12 +7,15 @@ buildPythonPackage rec {
   format = "other";
 
   src = fetchurl {
-    url = "https://fedorahosted.org/released/koji/koji-1.8.0.tar.bz2";
-    sha256 = "10dph209h4jgajb5jmbjhqy4z4hd22i7s2d93vm3ikdf01i8iwf1";
+    url = "https://github.com/koji-project/koji/archive/koji-1.8.0.tar.gz";
+    sha256 = "17rkipdxccdccbbb70f9wx91cq9713psmq23j7lgb4mlnwan926h";
   };
 
   propagatedBuildInputs = [ pycurl ];
 
+  # Judging from SyntaxError
+  disabled = isPy3k;
+
   makeFlags = "DESTDIR=$(out)";
 
   postInstall = ''

pkgs/development/python-modules/marshmallow-sqlalchemy/default.nix

@@ -0,0 +1,24 @@
+{ lib, buildPythonPackage, fetchPypi,
+  marshmallow, sqlalchemy
+}:
+
+buildPythonPackage rec {
+  pname = "marshmallow-sqlalchemy";
+  name = "${pname}-${version}";
+  version = "0.13.1";
+
+  meta = {
+    homepage = "https://github.com/marshmallow-code/marshmallow-sqlalchemy";
+    description = "SQLAlchemy integration with marshmallow ";
+    license = lib.licenses.mit;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0082ca2wwc9bymzkp1mr1l5h6rq0k1csv3vcq8ab24x0hdyg5qgk";
+  };
+
+  propagatedBuildInputs = [ marshmallow sqlalchemy ];
+
+  doCheck = false;
+}

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

@@ -0,0 +1,27 @@
+{ lib, buildPythonPackage, fetchPypi,
+  dateutil, simplejson
+}:
+
+buildPythonPackage rec {
+  pname = "marshmallow";
+  name = "${pname}-${version}";
+  version = "2.13.5";
+
+  meta = {
+    homepage = "https://github.com/marshmallow-code/marshmallow";
+    description = ''
+      A lightweight library for converting complex objects to and from
+      simple Python datatypes.
+    '';
+    license = lib.licenses.mit;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "048rzdkvnais51xdiy27nail5vxjb4ggw3vd60prn1q11lf16wig";
+  };
+
+  propagatedBuildInputs = [ dateutil simplejson ];
+
+  doCheck = false;
+}

pkgs/development/python-modules/parse-type/default.nix

@@ -0,0 +1,38 @@
+{ stdenv, fetchPypi, fetchpatch
+, buildPythonPackage, pythonOlder
+, pytest, pytestrunner
+, parse, six, enum34
+}:
+buildPythonPackage rec {
+  pname = "parse-type";
+  version = "0.3.4";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit version;
+    pname = "parse_type";
+    sha256 = "3dd0b323bafcb8c25e000ce5589042a1c99cba9c3bec77b9f591e46bc9606147";
+  };
+
+  patches = [
+    (fetchpatch {
+      name = "python-3.5-tests-compat.patch";
+      url = "https://github.com/jenisys/parse_type/pull/4.patch";
+      sha256 = "1mmn2fxss6q3qhaydd4s4v8vjgvgkg41v1vcivrzdsvgsc3npg7m";
+    })
+  ];
+
+  checkInputs = [ pytest pytestrunner ];
+  propagatedBuildInputs = [ parse six ] ++ stdenv.lib.optional (pythonOlder "3.4") enum34;
+
+  checkPhase = ''
+    py.test tests
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/jenisys/parse_type;
+    description = "Simplifies to build parse types based on the parse module";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ alunduil ];
+  };
+}

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

@@ -0,0 +1,32 @@
+{ stdenv, fetchPypi, fetchpatch
+, buildPythonPackage, python
+}:
+buildPythonPackage rec {
+  pname = "parse";
+  version = "1.6.6";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "71435aaac494e08cec76de646de2aab8392c114e56fe3f81c565ecc7eb886178";
+  };
+
+  patches = [
+    (fetchpatch {
+      name = "python-3.5-tests-compat.patch";
+      url = "https://github.com/r1chardj0n3s/parse/pull/34.patch";
+      sha256 = "16iicgkf3lwivmdnp3xkq4n87wjmr3nb77z8mwz67b7by9nnp3jg";
+    })
+  ];
+
+  checkPhase = ''
+    ${python.interpreter} test_parse.py
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/r1chardj0n3s/parse;
+    description = "parse() is the opposite of format()";
+    license = licenses.bsdOriginal;
+    maintainers = with maintainers; [ alunduil ];
+  };
+}

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

@@ -0,0 +1,25 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, nose
+, bcrypt
+}:
+
+buildPythonPackage rec {
+  pname = "passlib";
+  version = "1.7.1";
+  name    = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "3d948f64138c25633613f303bcc471126eae67c04d5e3f6b7b8ce6242f8653e0";
+  };
+
+  checkInputs = [ nose ];
+  propagatedBuildInputs = [ bcrypt ];
+
+  meta = {
+    description = "A password hashing library for Python";
+    homepage    = https://code.google.com/p/passlib/;
+  };
+}

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

@@ -0,0 +1,22 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+}:
+
+buildPythonPackage rec {
+  pname   = "pathspec";
+  version = "0.5.3";
+  name    = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "54478a66a360f4ebe4499c9235e4206fca5dec837b8e272d1ce37e0a626cc64d";
+  };
+
+  meta = {
+    description = "Utility library for gitignore-style pattern matching of file paths";
+    homepage = "https://github.com/cpburnz/python-path-specification";
+    license = lib.licenses.mpl20;
+    maintainers = with lib.maintainers; [ copumpkin ];
+  };
+}

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

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchPypi,
+  cssselect, cssutils, lxml, mock, nose, requests
+}:
+
+buildPythonPackage rec {
+  pname = "premailer";
+  name = "${pname}-${version}";
+  version = "3.0.1";
+
+  meta = {
+    description = "Turns CSS blocks into style attributes ";
+    homepage = https://github.com/peterbe/premailer;
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0cmlvqx1dvy16k5q5ylmr43nlfpb9k2zl3q7s4kzhf0lml4wqwaf";
+  };
+
+  buildInputs = [ mock nose ];
+  propagatedBuildInputs = [ cssselect cssutils lxml requests ];
+}

pkgs/development/python-modules/psd-tools/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildPythonPackage, fetchPypi,
+  docopt, pillow
+}:
+
+buildPythonPackage rec {
+  pname = "psd-tools";
+  name = "${pname}-${version}";
+  version = "1.4";
+
+  meta = {
+    description = "Python package for reading Adobe Photoshop PSD files";
+    homepage = https://github.com/kmike/psd-tools;
+    license = lib.licenses.mit;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0g2vss5hwlk96w0yj42n7ia56mly51n92f2rlbrifhn8hfbxd38s";
+  };
+
+  propagatedBuildInputs = [ docopt pillow ];
+}

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

@@ -0,0 +1,18 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "pycryptodomex";
+  name = "${pname}-${version}";
+  version = "3.4.5";
+
+  meta = {
+    description = "A self-contained cryptographic library for Python";
+    homepage = https://www.pycryptodome.org;
+    license = lib.licenses.bsd2;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1n5w5ls5syapmb39kavqgz2sa9pinzx4c9dvwa2147gj0hkh87wj";
+  };
+}

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

@@ -0,0 +1,28 @@
+{ stdenv, buildPythonApplication, fetchPypi
+, mock, pytest
+, six
+}:
+buildPythonApplication rec {
+  pname = "PyHamcrest";
+  version = "1.9.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "8ffaa0a53da57e89de14ced7185ac746227a8894dbd5a3c718bf05ddbd1d56cd";
+  };
+
+  checkInputs = [ mock pytest ];
+  propagatedBuildInputs = [ six ];
+
+  doCheck = false;  # pypi tarball does not include tests
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/hamcrest/PyHamcrest;
+    description = "Hamcrest framework for matcher objects";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [
+      alunduil
+    ];
+  };
+}

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

@@ -0,0 +1,23 @@
+{ lib, buildPythonPackage, fetchPypi,
+  future, pycryptodomex, pytest, requests, six
+}:
+
+buildPythonPackage rec {
+  pname = "pyjwkest";
+  name = "${pname}-${version}";
+  version = "1.3.2";
+
+  meta = {
+    description = "Implementation of JWT, JWS, JWE and JWK";
+    homepage = https://github.com/rohe/pyjwkest;
+    license = lib.licenses.asl20;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "11rrswsmma3wzi2qnmq929323yc6i9fkjsv8zr7b3vajd72yr49d";
+  };
+
+  buildInputs = [ pytest ];
+  propagatedBuildInputs = [ future pycryptodomex requests six ];
+}

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

@@ -1,42 +1,42 @@
-{ stdenv, fetchurl, buildPythonPackage, python, astroid, isort,
+{ stdenv, buildPythonPackage, fetchPypi, python, astroid, isort,
   pytest, pytestrunner,  mccabe, configparser, backports_functools_lru_cache }:
 
-  buildPythonPackage rec {
-    name = "${pname}-${version}";
-    pname = "pylint";
-    version = "1.7.2";
+buildPythonPackage rec {
+  name = "${pname}-${version}";
+  pname = "pylint";
+  version = "1.7.2";
 
-    src = fetchurl {
-      url = "mirror://pypi/p/${pname}/${name}.tar.gz";
-      sha256 = "ea6afb93a9ed810cf52ff3838eb3a15e2bf6a81b80de0eaede1ce442caa5ca69";
-    };
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "ea6afb93a9ed810cf52ff3838eb3a15e2bf6a81b80de0eaede1ce442caa5ca69";
+  };
 
-    buildInputs = [ pytest pytestrunner mccabe configparser backports_functools_lru_cache ];
+  buildInputs = [ pytest pytestrunner mccabe configparser backports_functools_lru_cache ];
 
-    propagatedBuildInputs = [ astroid configparser isort ];
+  propagatedBuildInputs = [ astroid configparser isort ];
 
-    postPatch = ''
-      # Remove broken darwin tests
-      sed -i -e '/test_parallel_execution/,+2d' pylint/test/test_self.py
-      sed -i -e '/test_py3k_jobs_option/,+4d' pylint/test/test_self.py
-      rm -vf pylint/test/test_functional.py
-    '';
+  postPatch = ''
+    # Remove broken darwin tests
+    sed -i -e '/test_parallel_execution/,+2d' pylint/test/test_self.py
+    sed -i -e '/test_py3k_jobs_option/,+4d' pylint/test/test_self.py
+    rm -vf pylint/test/test_functional.py
+  '';
 
-    checkPhase = ''
-      cd pylint/test
-      ${python.interpreter} -m unittest discover -p "*test*"
-    '';
+  checkPhase = ''
+    cd pylint/test
+    ${python.interpreter} -m unittest discover -p "*test*"
+  '';
 
-    postInstall = ''
-      mkdir -p $out/share/emacs/site-lisp
-      cp "elisp/"*.el $out/share/emacs/site-lisp/
-    '';
+  postInstall = ''
+    mkdir -p $out/share/emacs/site-lisp
+    cp "elisp/"*.el $out/share/emacs/site-lisp/
+  '';
 
-    meta = with stdenv.lib; {
-      homepage = http://www.logilab.org/project/pylint;
-      description = "A bug and style checker for Python";
-      platforms = platforms.all;
-      license = licenses.gpl1Plus;
-      maintainers = with maintainers; [ nand0p ];
-    };
-  }
+  meta = with stdenv.lib; {
+    homepage = http://www.logilab.org/project/pylint;
+    description = "A bug and style checker for Python";
+    platforms = platforms.all;
+    license = licenses.gpl1Plus;
+    maintainers = with maintainers; [ nand0p ];
+  };
+}

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

@@ -0,0 +1,31 @@
+{ lib, buildPythonPackage, fetchPypi,
+  nose, pytz, six, versiontools
+}:
+
+buildPythonPackage rec {
+  pname = "sampledata";
+  name = "${pname}-${version}";
+  version = "0.3.7";
+
+  meta = {
+    description = "Sample Data generator for Python ";
+    homepage = https://github.com/jespino/sampledata;
+    license = lib.licenses.bsd3;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1kx2j49lag30d32zhzsr50gl5b949wa4lcdap2filg0d07picsdh";
+  };
+
+  buildInputs = [ nose versiontools ];
+  propagatedBuildInputs = [ pytz six ];
+
+# ERROR: test_image_path_from_directory (tests.tests.TestImageHelpers)
+# ERROR: test_image_stream (tests.tests.TestImageHelpers)
+  doCheck = false;
+
+  checkPhase = ''
+    nosetests -e "TestImageHelpers"
+  '';
+}

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

@@ -0,0 +1,27 @@
+{ stdenv, fetchFromGitHub, buildPythonPackage
+, dbus-python, cryptography }:
+
+buildPythonPackage rec {
+  pname = "secretstorage";
+  version = "2.3.1";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "mitya57";
+    repo = "secretstorage";
+    rev = version;
+    sha256 = "1sjd2jjbxgkkxyrfwx89x0hsnn39w2cr2qkxbg1iz52znr4sqism";
+  };
+
+  propagatedBuildInputs = [ dbus-python cryptography ];
+
+  doCheck = false; # requires dbus session
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/mitya57/secretstorage";
+    description = "Python bindings to FreeDesktop.org Secret Service API";
+    license = licenses.bsdOriginal;
+    platforms = platforms.linux;
+    maintainer = with maintainers; [ teto ];
+  };
+}

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

@@ -0,0 +1,26 @@
+{ lib, buildPythonPackage, fetchPypi,
+  flake8, py, pyflakes, six, tox
+}:
+
+buildPythonPackage rec {
+  pname = "serpy";
+  name = "${pname}-${version}";
+  version = "0.1.1";
+
+  meta = {
+    description = "ridiculously fast object serialization";
+    homepage = https://github.com/clarkduvall/serpy;
+    license = lib.licenses.mit;
+  };
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0r9wn99x9nbqxfancnq9jh3cn83i1b6gc79xj0ipnxixp661yj5i";
+  };
+
+  buildInputs = [ flake8 py pyflakes tox ];
+  propagatedBuildInputs = [ six ];
+
+  # ImportError: No module named 'tests
+  doCheck = false;
+}

pkgs/development/python-modules/urllib3/default.nix

@@ -1,5 +1,6 @@
 { stdenv, buildPythonPackage, fetchPypi
-, coverage, tornado, mock, nose, psutil, pysocks }:
+, pytest, mock, tornado, pyopenssl, cryptography
+, idna, certifi, ipaddress, pysocks }:
 
 buildPythonPackage rec {
   pname = "urllib3";
@@ -22,11 +23,12 @@ buildPythonPackage rec {
 
   doCheck = false;
 
-  buildInputs = [ coverage tornado mock nose psutil pysocks ];
+  checkInputs = [ pytest mock tornado ];
+  propagatedBuildInputs = [ pyopenssl cryptography idna certifi ipaddress pysocks ];
 
   meta = with stdenv.lib; {
-    description = "A Python library for Dropbox's HTTP-based Core and Datastore APIs";
-    homepage = https://www.dropbox.com/developers/core/docs;
+    description = "Powerful, sanity-friendly HTTP client for Python";
+    homepage = https://github.com/shazow/urllib3;
     license = licenses.mit;
   };
 }

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

@@ -1,5 +1,5 @@
 { stdenv, buildPythonPackage, fetchPypi
-, nose, pyyaml }:
+, nose, pyyaml, pathspec }:
 
 buildPythonPackage rec {
   pname = "yamllint";
@@ -11,9 +11,12 @@ buildPythonPackage rec {
     sha256 = "048743567ca9511e19222233ebb53795586a2cede07b79e801577e0a9b4f173c";
   };
 
-  buildInputs = [ nose ];
+  checkInputs = [ nose ];
 
-  propagatedBuildInputs = [  pyyaml ];
+  propagatedBuildInputs = [  pyyaml pathspec ];
+
+  # Two test failures
+  doCheck = false;
 
   meta = with stdenv.lib; {
     description = "A linter for YAML files";

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

@@ -5,18 +5,18 @@
 buildPythonPackage rec {
   name = "${pname}-${version}";
   pname = "zetup";
-  version = "0.2.42";
+  version = "0.2.34";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "6c9e25249f3014ed2162398772ccf1a5e8a4e9e66c74e3c7f6683945a6a3d84c";
+    sha256 = "0k4lm51b5qjy7yxy3n5z8vc5hlvjcsfsvwjgqzkr0pisysar1kpf";
   };
 
   checkPhase = ''
     py.test test
   '';
 
-  buildInputs = [ pytest pathpy nbconvert ];
+  checkInputs = [ pytest pathpy nbconvert ];
   propagatedBuildInputs = [ setuptools_scm ];
 
   meta = with stdenv.lib; {

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

@@ -1,18 +1,41 @@
-{ stdenv, pythonPackages }:
+{ stdenv, python }:
 
-pythonPackages.buildPythonApplication rec {
-  name = "${pname}-${version}";
-  version = "0.21.2";
-  pname = "conan";
-
-  src = pythonPackages.fetchPypi {
-    inherit pname version;
-    sha256 = "0x9s5h81d885xdrjw5x99q18lhmj11kalrs6xnjy2phrr8qzil8c";
+let
+  p = python.override {
+    packageOverrides = self: super: {
+      astroid = super.astroid.overridePythonAttrs (oldAttrs: rec {
+        version = "1.4.9";
+        name = "${oldAttrs.pname}-${version}";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "a483e7891ce3a06dadfc6cb9095b0938aca58940d43576d72e4502b480c085d7";
+        };
+      });
+      pylint = super.pylint.overridePythonAttrs (oldAttrs: rec {
+        version = "1.6.5";
+        name = "${oldAttrs.pname}-${version}";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "a673984a8dd78e4a8b8cfdee5359a1309d833cf38405008f4a249994a8456719";
+        };
+      });
+    };
   };
 
-  propagatedBuildInputs = with pythonPackages; [
+in p.pkgs.buildPythonApplication rec {
+  name = "${pname}-${version}";
+  version = "0.26.1";
+  pname = "conan";
+
+  src = p.pkgs.fetchPypi {
+    inherit pname version;
+    sha256 = "2da5a140a74d912d5561698b8cc5a5e5583b9dbe36623c59b4ce4be586476e7c";
+  };
+
+  propagatedBuildInputs = with p.pkgs; [
     requests fasteners pyyaml pyjwt colorama patch
     bottle pluginbase six distro pylint node-semver
+    future pygments mccabe
   ];
 
   # enable tests once all of these pythonPackages available:

pkgs/tools/admin/mycli/default.nix

@@ -0,0 +1,38 @@
+{ lib
+, python
+}:
+
+with python.pkgs;
+
+buildPythonApplication rec {
+  pname = "mycli";
+  version = "1.6.0";
+  name = "${pname}-${version}";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0qg4b62kizyb16kk0cvpk70bfs3gg4q4hj2b15nnc7a3gqqfp67j";
+  };
+
+  propagatedBuildInputs = [
+    pymysql configobj sqlparse prompt_toolkit pygments click pycrypto
+  ];
+
+  postPatch = ''
+    substituteInPlace setup.py --replace "==" ">="
+  '';
+
+  # No tests in archive. Newer versions do include tests
+  doCheck = false;
+
+  meta = {
+    inherit version;
+    description = "Command-line interface for MySQL";
+    longDescription = ''
+      Rich command-line interface for MySQL with auto-completion and
+      syntax highlighting.
+    '';
+    homepage = http://mycli.net;
+    license = lib.licenses.bsd3;
+  };
+}

pkgs/tools/misc/diffoscope/default.nix

@@ -1,25 +1,24 @@
-{ lib, stdenv, fetchgit, fetchpatch, python3, docutils
+{ lib, stdenv, fetchgit, fetchpatch, python3Packages, docutils
 , acl, binutils, bzip2, cbfstool, cdrkit, colord, cpio, diffutils, e2fsprogs, file, fpc, gettext, ghc
-, gnupg1, gzip, jdk, libcaca, mono, pdftk, poppler_utils, sng, sqlite, squashfsTools, unzip, vim, xz
+, gnupg1, gzip, jdk, libcaca, mono, pdftk, poppler_utils, sng, sqlite, squashfsTools, unzip, xxd, xz
 , colordiff
 , enableBloat ? false
 }:
 
-python3.pkgs.buildPythonApplication rec {
-  pname = "diffoscope";
-  name = "${pname}-${version}";
-  version = "77";
+python3Packages.buildPythonApplication rec {
+  name = "diffoscope-${version}";
+  version = "85";
 
   src = fetchgit {
-    url = "git://anonscm.debian.org/reproducible/diffoscope.git";
-    rev = "refs/tags/${version}";
-    sha256 = "0l5q24sqb88qkz62cz85bq65myfqig3z3m1lj2s92hdlqip9946b";
+    url    = "git://anonscm.debian.org/reproducible/diffoscope.git";
+    rev    = "refs/tags/${version}";
+    sha256 = "0kmcfhgva1fl6x5b07sc7k6ba9mqs3ma0lvspxm31w7nrrrqcvlr";
   };
 
-  patches =
-    [ # Ignore different link counts.
-      ./ignore_links.patch
-    ];
+  patches = [
+    # Ignore different link counts - doesn't work with 85
+    # ./ignore_links.patch
+  ];
 
   postPatch = ''
     # Upstream doesn't provide a PKG-INFO file
@@ -28,10 +27,9 @@ python3.pkgs.buildPythonApplication rec {
 
   # Still missing these tools: enjarify, otool & lipo (maybe macOS only), showttf
   # Also these libraries: python3-guestfs
-  # FIXME: move xxd into a separate package so we don't have to pull in all of vim.
-  pythonPath = with python3.pkgs;
+  pythonPath = with python3Packages;
     [ debian libarchive-c python_magic tlsh rpm cdrkit acl binutils bzip2 cbfstool cpio diffutils e2fsprogs file gettext
-      gzip libcaca poppler_utils sng sqlite squashfsTools unzip vim xz colordiff
+      gzip libcaca poppler_utils sng sqlite squashfsTools unzip xxd xz colordiff
     ] ++ lib.optionals enableBloat [ colord fpc ghc gnupg1 jdk mono pdftk ];
 
   doCheck = false; # Calls 'mknod' in squashfs tests, which needs root
@@ -53,9 +51,9 @@ python3.pkgs.buildPythonApplication rec {
       diffoscope is developed as part of the "reproducible builds" Debian
       project and was formerly known as "debbindiff".
     '';
-    homepage = https://wiki.debian.org/ReproducibleBuilds;
-    license = licenses.gpl3Plus;
-    maintainers = [ maintainers.dezgeg ];
-    platforms = platforms.linux;
+    homepage    = https://wiki.debian.org/ReproducibleBuilds;
+    license     = licenses.gpl3Plus;
+    maintainers = with maintainers; [ dezgeg ];
+    platforms   = platforms.linux;
   };
 }

pkgs/tools/networking/gmvault/default.nix

@@ -21,6 +21,7 @@ pythonPackages.buildPythonApplication rec {
     cat ${startScript} > etc/scripts/gmvault
     chmod +x etc/scripts/gmvault
     substituteInPlace setup.py --replace "==" ">="
+    substituteInPlace setup.py --replace "argparse" ""
   '';
 
   meta = {

pkgs/tools/networking/mitmproxy/default.nix

@@ -1,6 +1,27 @@
-{ stdenv, fetchpatch, fetchFromGitHub, python3Packages, glibcLocales }:
+{ stdenv, fetchpatch, fetchFromGitHub, python3, glibcLocales }:
 
-python3Packages.buildPythonPackage rec {
+let
+  p = python3.override {
+    packageOverrides = self: super: {
+      cryptography = super.cryptography.overridePythonAttrs (oldAttrs: rec {
+        version = "1.8.2";
+        name = "${oldAttrs.pname}-${version}";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "8e88ebac371a388024dab3ccf393bf3c1790d21bc3c299d5a6f9f83fb823beda";
+        };
+      });
+      cryptography_vectors = super.cryptography_vectors.overridePythonAttrs (oldAttrs: rec {
+        version = self.cryptography.version;
+        name = "${oldAttrs.pname}-${version}";
+        src = oldAttrs.src.override {
+          inherit version;
+          sha256 = "00daa04c9870345f56605d91d7d4897bc1b16f6fff7c74cb602b08ef16c0fb43";
+        };
+      });
+    };
+  };
+in p.pkgs.buildPythonPackage rec {
   baseName = "mitmproxy";
   name = "${baseName}-${version}";
   version = "2.0.2";
@@ -33,7 +54,7 @@ python3Packages.buildPythonPackage rec {
     LC_CTYPE=en_US.UTF-8 pytest -k 'not test_echo'
   '';
 
-  propagatedBuildInputs = with python3Packages; [
+  propagatedBuildInputs = with p.pkgs; [
     blinker click certifi construct cryptography
     cssutils editorconfig h2 html2text hyperframe
     jsbeautifier kaitaistruct passlib pyasn1 pyopenssl
@@ -41,7 +62,7 @@ python3Packages.buildPythonPackage rec {
     urwid watchdog brotlipy sortedcontainers
   ];
 
-  buildInputs = with python3Packages; [
+  buildInputs = with p.pkgs; [
     beautifulsoup4 flask pytz pytest pytestrunner protobuf3_2 glibcLocales
   ];
 

pkgs/tools/security/pinentry-mac/default.nix

@@ -6,8 +6,8 @@ stdenv.mkDerivation rec {
   src = fetchFromGitHub {
     owner = "matthewbauer";
     repo = "pinentry-mac";
-    rev = "d60aa902644a1f0126ec50e79937423a3a7c3bc4";
-    sha256 = "0xp4rdyj0mw6gg1z1wraggb1qlkjb5845mibrz3nj0l692da52nq";
+    rev = "6dfef256c8ea32d642fea847f27d800f024cf51e";
+    sha256 = "0g75302697gqcxyf2hyqzvcbd5pyss1bl2xvfd40wqav7dlyvj83";
   };
 
   buildInputs = [ xcbuild libiconv Cocoa ncurses ];

pkgs/top-level/all-packages.nix

@@ -1563,6 +1563,10 @@ with pkgs;
     cudatoolkit = cudatoolkit8;
   };
 
+  cudnn60_cudatoolkit80 = callPackage ../development/libraries/science/math/cudnn/8.0-6.0 {
+    cudatoolkit = cudatoolkit8;
+  };
+
   curlFull = curl.override {
     idnSupport = true;
     ldapSupport = true;
@@ -3345,6 +3349,8 @@ with pkgs;
 
   munge = callPackage ../tools/security/munge { };
 
+  mycli = callPackage ../tools/admin/mycli { };
+
   mysql2pgsql = callPackage ../tools/misc/mysql2pgsql { };
 
   mysqltuner = callPackage ../tools/misc/mysqltuner { };
@@ -10000,10 +10006,9 @@ with pkgs;
 
   protobuf = protobuf2_6;
   protobuf3_0 = lowPrio (callPackage ../development/libraries/protobuf/3.0.nix { });
-  # 3.0.0-beta-2 is only introduced for tensorflow. remove this version when tensorflow is moved to 3.0.
-  protobuf3_0_0b2 = lowPrio (callPackage ../development/libraries/protobuf/3.0.0-beta-2.nix { });
   protobuf3_1 = callPackage ../development/libraries/protobuf/3.1.nix { };
   protobuf3_2 = callPackage ../development/libraries/protobuf/3.2.nix { };
+  protobuf3_3 = callPackage ../development/libraries/protobuf/3.3.nix { };
   protobuf2_6 = callPackage ../development/libraries/protobuf/2.6.nix { };
   protobuf2_5 = callPackage ../development/libraries/protobuf/2.5.nix { };
 
@@ -13384,7 +13389,7 @@ with pkgs;
   abook = callPackage ../applications/misc/abook { };
 
   acd-cli = callPackage ../applications/networking/sync/acd_cli {
-    inherit (python35Packages)
+    inherit (python3Packages)
       buildPythonApplication appdirs colorama dateutil
       requests requests_toolbelt sqlalchemy fusepy;
   };
@@ -18211,6 +18216,9 @@ with pkgs;
     version = "8.5pl3";
   };
   coq_8_6 = callPackage ../applications/science/logic/coq {};
+  coq_8_7 = callPackage ../applications/science/logic/coq {
+    version = "8.7+beta1";
+  };
   coq_HEAD = callPackage ../applications/science/logic/coq/HEAD.nix {};
 
   mkCoqPackages_8_4 = self: let callPackage = newScope self; in {
@@ -18393,6 +18401,8 @@ with pkgs;
 
   ### SCIENCE / ELECTRONICS
 
+  adms = callPackage ../applications/science/electronics/adms { };
+
   eagle = callPackage ../applications/science/electronics/eagle { };
 
   caneda = callPackage ../applications/science/electronics/caneda { };
@@ -18416,6 +18426,7 @@ with pkgs;
 
   qucs = callPackage ../applications/science/electronics/qucs { };
 
+
   xoscope = callPackage ../applications/science/electronics/xoscope { };
 
 

pkgs/top-level/python-packages.nix

@@ -117,8 +117,12 @@ in {
 
   agate-sql = callPackage ../development/python-modules/agate-sql { };
 
+  aioamqp = callPackage ../development/python-modules/aioamqp { };
+
   ansicolor = callPackage ../development/python-modules/ansicolor { };
 
+  asana = callPackage ../development/python-modules/asana { };
+
   asn1crypto = callPackage ../development/python-modules/asn1crypto { };
 
   astropy = callPackage ../development/python-modules/astropy {  };
@@ -169,6 +173,8 @@ in {
 
   distorm3 = callPackage ../development/python-modules/distorm3 { };
 
+  diff-match-patch = callPackage ../development/python-modules/diff-match-patch { };
+
   h5py = callPackage ../development/python-modules/h5py {
     hdf5 = pkgs.hdf5;
   };
@@ -219,6 +225,8 @@ in {
 
   pycryptodome = callPackage ../development/python-modules/pycryptodome { };
 
+  pycryptodomex = callPackage ../development/python-modules/pycryptodomex { };
+
   PyChromecast = callPackage ../development/python-modules/pychromecast {
     protobuf = self.protobuf3_2;
   };
@@ -243,6 +251,8 @@ in {
     libglade = pkgs.gnome2.libglade;
   };
 
+  pyjwkest = callPackage ../development/python-modules/pyjwkest { };
+
   pyqt4 = callPackage ../development/python-modules/pyqt/4.x.nix {
     pythonPackages = self;
   };
@@ -2634,34 +2644,6 @@ in {
 
   characteristic = callPackage ../development/python-modules/characteristic { };
 
-  # This package is no longer actively maintained and can be removed if it becomes broken.
-  cgkit = buildPythonPackage rec {
-    version = "2.0.0";
-    name = "cgkit-${version}";
-    disabled = isPy3k;
-
-    src = pkgs.fetchurl {
-      url = "mirror://sourceforge/project/cgkit/cgkit/cgkit-${version}/cgkit-${version}-py2k.tar.gz";
-      sha256 = "0vvllc42mdyma3c7yqhahs4bfxymm2kvmc4va7dxqr5x0rzh6rd6";
-    };
-
-    patches = [ ../development/python-modules/cgkit/scons-env.patch ];
-
-    buildInputs = with pkgs; [ scons boost mesa ];
-
-    preBuild = ''
-      cd supportlib
-      scons
-      cd -
-    '';
-
-    meta = {
-      homepage = http://cgkit.sourceforge.net;
-      description = "Python Computer Graphics Kit";
-      maintainers = with maintainers; [ expipiplus1 ];
-    };
-  };
-
   cheetah = buildPythonPackage rec {
     version = "2.4.4";
     name = "cheetah-${version}";
@@ -5196,6 +5178,7 @@ in {
       sha256 = "0bixx80zjq0286dwm4zhg8bdhc8pqlrqy4n2jg7i6m6a4gv4gak5";
     };
 
+    buildInputs = with self; [ pytestrunner ];
     propagatedBuildInputs = with self; [ requests urllib3 mock setuptools ];
 
     meta = {
@@ -5258,6 +5241,8 @@ in {
     };
   };
 
+  easy-thumbnails = callPackage ../development/python-modules/easy-thumbnails { };
+
   eccodes = if (isPy27) then
       (pkgs.eccodes.overrideAttrs (oldattrs: {
     name = "${python.libPrefix}-" + oldattrs.name;
@@ -7151,23 +7136,7 @@ in {
     };
   };
 
-  pathspec = buildPythonPackage rec {
-    pname   = "pathspec";
-    version = "0.5.2";
-    name    = "${pname}-${version}";
-
-    src = self.fetchPypi {
-      inherit pname version;
-      sha256 = "f9fdf4408f4adb30e9f507f61d3a41c968e9c6e6c519d4bbd2a189627b5e86f0";
-    };
-
-    meta = {
-      description = "Utility library for gitignore-style pattern matching of file paths";
-      homepage = "https://github.com/cpburnz/python-path-specification";
-      license = licenses.mpl20;
-      maintainers = with maintainers; [ copumpkin ];
-    };
-  };
+  pathspec = callPackage ../development/python-modules/pathspec { };
 
   pathtools = buildPythonPackage rec {
     name = "pathtools-${version}";
@@ -7210,23 +7179,7 @@ in {
     };
   };
 
-  passlib = buildPythonPackage rec {
-    version = "1.6.5";
-    name    = "passlib-${version}";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/passlib/passlib-${version}.tar.gz";
-      sha256 = "1z27wdxs5rj5xhhqfzvzn3yg682irkxw6dcs5jj7mcf97psk8gd8";
-    };
-
-    buildInputs = with self; [ nose ];
-    propagatedBuildInputs = with self; [ bcrypt ];
-
-    meta = {
-      description = "A password hashing library for Python";
-      homepage    = https://code.google.com/p/passlib/;
-    };
-  };
+  passlib = callPackage ../development/python-modules/passlib { };
 
   path-and-address = buildPythonPackage rec {
     version = "2.0.1";
@@ -8623,8 +8576,22 @@ in {
 
   django_guardian = callPackage ../development/python-modules/django_guardian.nix { };
 
+  django-ipware = callPackage ../development/python-modules/django-ipware { };
+
+  django-jinja = callPackage ../development/python-modules/django-jinja2 { };
+
+  django-pglocks = callPackage ../development/python-modules/django-pglocks { };
+
+  django-picklefield = callPackage ../development/python-modules/django-picklefield { };
+
   django_polymorphic = callPackage ../development/python-modules/django-polymorphic { };
 
+  django-sampledatahelper = callPackage ../development/python-modules/django-sampledatahelper { };
+
+  django-sites = callPackage ../development/python-modules/django-sites { };
+
+  django-sr = callPackage ../development/python-modules/django-sr { };
+
   django_tagging = callPackage ../development/python-modules/django_tagging { };
 
   django_tagging_0_3 = self.django_tagging.overrideAttrs (attrs: rec {
@@ -8874,6 +8841,8 @@ in {
     };
   };
 
+  djmail = callPackage ../development/python-modules/djmail { };
+
   pillowfight = buildPythonPackage rec {
     name = "pillowfight-${version}";
     version = "0.2";
@@ -9441,6 +9410,10 @@ in {
 
   flask_ldap_login = callPackage ../development/python-modules/flask-ldap-login.nix { };
 
+  flask_mail = callPackage ../development/python-modules/flask-mail { };
+
+  flask_marshmallow = callPackage ../development/python-modules/flask-marshmallow { };
+
   flask_migrate = callPackage ../development/python-modules/flask-migrate { };
 
   flask_oauthlib = callPackage ../development/python-modules/flask-oauthlib.nix { };
@@ -9706,6 +9679,8 @@ in {
     };
   });
 
+  fn = callPackage ../development/python-modules/fn { };
+
   folium = callPackage ../development/python-modules/folium { };
 
   fontforge = pkgs.fontforge.override {
@@ -11139,6 +11114,8 @@ in {
 
   jsonnet = buildPythonPackage {
     inherit (pkgs.jsonnet) name src;
+    # Python 3 is not yet supported https://github.com/google/jsonnet/pull/335
+    disabled = isPy3k;
   };
 
   jupyter_client = callPackage ../development/python-modules/jupyter_client { };
@@ -11874,6 +11851,10 @@ in {
     };
   };
 
+  marshmallow = callPackage ../development/python-modules/marshmallow { };
+
+  marshmallow-sqlalchemy = callPackage ../development/python-modules/marshmallow-sqlalchemy { };
+
   manuel = buildPythonPackage rec {
     name = "manuel-${version}";
     version = "1.8.0";
@@ -11893,12 +11874,12 @@ in {
   };
 
   markdown = buildPythonPackage rec {
-    version = "2.6.7";
+    version = "2.6.8";
     name = "markdown-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/M/Markdown/Markdown-${version}.tar.gz";
-      sha256 = "1h055llfd0ps0ig7qb3v1j9068xv90dc9s7xkhkgz9zg8r4g5sys";
+      sha256 = "0cqfhr1km2s5d8jm6hbwgkrrj9hvkjf2gab3s2axlrw1clgaij0a";
     };
 
     # error: invalid command 'test'
@@ -15496,7 +15477,7 @@ in {
       sha256 = "1vmyvynqzx5zvbipaxff4fnzy3h3dvl3zicyr15yb816j93jl2ca";
     };
 
-    buildInputs = with self; [ mock nose pep8 pylint ];
+    buildInputs = with self; [ mock nose pep8 pylint mccabe ];
 
     meta = {
       description = "RabbitMQ Focused AMQP low-level library";
@@ -15973,39 +15954,6 @@ in {
     };
   };
 
-
-  mycli = buildPythonPackage rec {
-    name = "mycli-${version}";
-    version = "1.6.0";
-    disabled = isPy35;
-
-    src = pkgs.fetchFromGitHub {
-      sha256 = "0vvl36gxawa0h36v119j47fdylj8k73ak6hv04s5cjqn5adcjjbh";
-      rev = "v${version}";
-      repo = "mycli";
-      owner = "dbcli";
-    };
-
-    propagatedBuildInputs = with self; [
-      pymysql configobj sqlparse prompt_toolkit pygments click pycrypto
-    ];
-
-    postPatch = ''
-      substituteInPlace setup.py --replace "==" ">="
-    '';
-
-    meta = {
-      inherit version;
-      description = "Command-line interface for MySQL";
-      longDescription = ''
-        Rich command-line interface for MySQL with auto-completion and
-        syntax highlighting.
-      '';
-      homepage = http://mycli.net;
-      license = licenses.bsd3;
-    };
-  };
-
   pickleshare = buildPythonPackage rec {
     version = "0.7.4";
     name = "pickleshare-${version}";
@@ -16397,6 +16345,8 @@ in {
     };
   };
 
+  premailer = callPackage ../development/python-modules/premailer { };
+
   prettytable = buildPythonPackage rec {
     name = "prettytable-0.7.1";
 
@@ -16437,7 +16387,11 @@ in {
   });
 
   protobuf = self.protobuf2_6;
-  # only required by tensorflow
+  protobuf3_3 = callPackage ../development/python-modules/protobuf.nix {
+    disabled = isPyPy;
+    doCheck = !isPy3k;
+    protobuf = pkgs.protobuf3_3;
+  };
   protobuf3_2 = callPackage ../development/python-modules/protobuf.nix {
     disabled = isPyPy;
     doCheck = !isPy3k;
@@ -16458,6 +16412,8 @@ in {
     protobuf = pkgs.protobuf2_5;
   };
 
+  psd-tools = callPackage ../development/python-modules/psd-tools { };
+
   psutil = buildPythonPackage rec {
     name = "psutil-${version}";
     version = "4.3.0";
@@ -16870,7 +16826,7 @@ in {
     preConfigure = ''
       substituteInPlace setup.py \
         --replace '"/usr/include"' '"${pkgs.gdb}/include"' \
-        --replace '"/usr/lib"' '"${pkgs.binutils.out}/lib"'
+        --replace '"/usr/lib"' '"${pkgs.binutils.lib}/lib"'
     '';
 
     meta = {
@@ -20037,6 +19993,8 @@ in {
     propagatedBuildInputs = [ self.cffi ];
   };
 
+  sampledata = callPackage ../development/python-modules/sampledata { };
+
   scapy = buildPythonPackage rec {
     name = "scapy-2.2.0";
 
@@ -20161,6 +20119,8 @@ in {
     '';
   };
 
+  serpy = callPackage ../development/python-modules/serpy { };
+
   setuptools_scm = callPackage ../development/python-modules/setuptools_scm { };
 
   setuptoolsDarcs = buildPythonPackage rec {
@@ -20904,6 +20864,8 @@ in {
     };
   };
 
+  secretstorage = callPackage ../development/python-modules/secretstorage { };
+
   semantic = buildPythonPackage rec {
     name = "semantic-1.0.3";
 
@@ -23991,11 +23953,11 @@ EOF
 
   libarchive-c = buildPythonPackage rec {
     name = "libarchive-c-${version}";
-    version = "2.5";
+    version = "2.7";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/l/libarchive-c/${name}.tar.gz";
-      sha256 = "98660daa2501d2da51ab6f39893dc24e88916e72b2d80c205641faa5bce66859";
+      sha256 = "011bfsmqpcwd6920kckllh7zhw2y4rrasgmddb7wjzn2hg1xpsjn";
     };
 
     LC_ALL="en_US.UTF-8";
@@ -24005,7 +23967,7 @@ EOF
         "find_library('archive')" "'${pkgs.libarchive.lib}/lib/libarchive.so'"
     '';
     checkPhase = ''
-      py.test tests -k 'not test_check_archiveentry_with_unicode_entries_and_name_zip'
+      py.test tests -k 'not test_check_archiveentry_with_unicode_entries_and_name_zip and not test_check_archiveentry_using_python_testtar'
     '';
 
     buildInputs = with self; [ pytest pkgs.glibcLocales ];
@@ -27522,9 +27484,20 @@ EOF
 
   preshed = callPackage ../development/python-modules/preshed { };
 
+  backports_weakref = callPackage ../development/python-modules/backports_weakref { }; 
+
   thinc = callPackage ../development/python-modules/thinc { };
 
   spacy = callPackage ../development/python-modules/spacy { };
+
+  behave = callPackage ../development/python-modules/behave { };
+
+  pyhamcrest = callPackage ../development/python-modules/pyhamcrest { };
+ 
+  parse = callPackage ../development/python-modules/parse { };
+
+  parse-type = callPackage ../development/python-modules/parse-type { };
+
 });
 
 in fix' (extends overrides packages)