Merge branch 'master' into staging-next

A couple thousand rebuilds have accumulated on master.

lib/default.nix

@@ -132,6 +132,7 @@ let
       mergeAttrsWithFunc mergeAttrsConcatenateValues
       mergeAttrsNoOverride mergeAttrByFunc mergeAttrsByFuncDefaults
       mergeAttrsByFuncDefaultsClean mergeAttrBy
+      fakeSha256 fakeSha512
       nixType imap;
   });
 in lib

lib/deprecated.nix

@@ -270,4 +270,8 @@ rec {
      starting at zero.
   */
   imap = imap1;
+
+  # Fake hashes. Can be used as hash placeholders, when computing hash ahead isn't trivial
+  fakeSha256 = "0000000000000000000000000000000000000000000000000000000000000000";
+  fakeSha512 = "00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000";
 }

maintainers/maintainer-list.nix

@@ -475,6 +475,11 @@
     github = "bandresen";
     name = "Benjamin Andresen";
   };
+  baracoder = {
+    email = "baracoder@googlemail.com";
+    github = "baracoder";
+    name = "Herman Fries";
+  };
   barrucadu = {
     email = "mike@barrucadu.co.uk";
     github = "barrucadu";
@@ -1953,6 +1958,11 @@
     github = "jakelogemann";
     name = "Jake Logemann";
   };
+  jakewaksbaum = {
+    email = "jake.waksbaum@gmail.com";
+    github = "jbaum98";
+    name = "Jake Waksbaum";
+  };
   jammerful = {
     email = "jammerful@gmail.com";
     github = "jammerful";
@@ -3062,6 +3072,11 @@
     github = "nadrieril";
     name = "Nadrieril Feneanar";
   };
+  nalbyuites = {
+    email = "ashijit007@gmail.com";
+    github = "nalbyuites";
+    name = "Ashijit Pramanik";
+  };
   namore = {
     email = "namor@hemio.de";
     github = "namore";
@@ -4351,6 +4366,11 @@
     github = "tazjin";
     name = "Vincent Ambo";
   };
+  tbenst = {
+    email = "nix@tylerbenster.com";
+    github = "tbenst";
+    name = "Tyler Benster";
+  };
   teh = {
     email = "tehunger@gmail.com";
     github = "teh";

nixos/modules/installer/tools/nix-fallback-paths.nix

@@ -1,6 +1,6 @@
 {
-  x86_64-linux = "/nix/store/cdcia67siabmj6li7vyffgv2cry86fq8-nix-2.1.3";
+  x86_64-linux = "/nix/store/pid1yakjasch4pwl63nzbj22z9zf0q26-nix-2.2";
-  i686-linux = "/nix/store/6q3xi6y5qnsv7d62b8n00hqfxi8rs2xs-nix-2.1.3";
+  i686-linux = "/nix/store/qpkl0cxy0xh4h432lv2qsjrmhvx5x2vy-nix-2.2";
-  aarch64-linux = "/nix/store/2v93d0vimlm28jg0ms6v1i6lc0fq13pn-nix-2.1.3";
+  aarch64-linux = "/nix/store/0jg7h94x986d8cskg6gcfza9x67spdbp-nix-2.2";
-  x86_64-darwin = "/nix/store/dkjlfkrknmxbjmpfk3dg4q3nmb7m3zvk-nix-2.1.3";
+  x86_64-darwin = "/nix/store/a48whqkmxnsfhwbk6nay74iyc1cf0lr2-nix-2.2";
 }

nixos/modules/services/backup/borgbackup.nix

@@ -191,10 +191,9 @@ in {
         options = {
 
           paths = mkOption {
-            type = with types; either path (listOf str);
+            type = with types; coercedTo str lib.singleton (listOf str);
             description = "Path(s) to back up.";
             example = "/home/user";
-            apply = x: if isList x then x else [ x ];
           };
 
           repo = mkOption {

nixos/tests/all-tests.nix

@@ -109,7 +109,7 @@ in
   ipv6 = handleTest ./ipv6.nix {};
   jenkins = handleTest ./jenkins.nix {};
   #kafka = handleTest ./kafka.nix {}; # broken since openjdk: 8u181 -> 8u192
-  kerberos = handleTest tests/kerberos/default.nix {};
+  kerberos = handleTest ./kerberos/default.nix {};
   kernel-latest = handleTest ./kernel-latest.nix {};
   kernel-lts = handleTest ./kernel-lts.nix {};
   keymap = handleTest ./keymap.nix {};

nixos/tests/docker-tools.nix

@@ -62,6 +62,7 @@ import ./make-test.nix ({ pkgs, ... }: {
       # Ensure Layered Docker images work
       $docker->succeed("docker load --input='${pkgs.dockerTools.examples.layered-image}'");
       $docker->succeed("docker run --rm ${pkgs.dockerTools.examples.layered-image.imageName}");
+      $docker->succeed("docker run --rm ${pkgs.dockerTools.examples.layered-image.imageName} cat extraCommands");
 
       # Ensure building an image on top of a layered Docker images work
       $docker->succeed("docker load --input='${pkgs.dockerTools.examples.layered-on-top}'");

nixos/tests/kerberos/default.nix

@@ -1,5 +1,7 @@
-{ system ? builtins.currentSystem }:
+{ system ? builtins.currentSystem
+, pkgs ? import ../../.. { inherit system; }
+}:
 {
-  mit = import ./mit.nix { inherit system; };
+  mit = import ./mit.nix { inherit system pkgs; };
-  heimdal = import ./heimdal.nix { inherit system; };
+  heimdal = import ./heimdal.nix { inherit system pkgs; };
 }

nixos/tests/nexus.nix

@@ -14,7 +14,7 @@ import ./make-test.nix ({ pkgs, ...} : {
     server =
       { ... }:
       { virtualisation.memorySize = 2047; # qemu-system-i386 has a 2047M limit
-        virtualisation.diskSize = 2048;
+        virtualisation.diskSize = 8192;
 
         services.nexus.enable = true;
       };

pkgs/applications/editors/emacs-modes/elpa-generated.nix

@@ -163,10 +163,10 @@
       elpaBuild {
         pname = "arbitools";
         ename = "arbitools";
-        version = "0.95";
+        version = "0.97";
         src = fetchurl {
-          url = "https://elpa.gnu.org/packages/arbitools-0.95.el";
+          url = "https://elpa.gnu.org/packages/arbitools-0.97.el";
-          sha256 = "1v6i9d35xqag9a8j12n3xjircwzndjwgb84qm7rsgbns60v3ci8y";
+          sha256 = "0fx1z4mw3v42xzixsj80xw56pg00bch04galkjbxbqzm25nl4aha";
         };
         packageRequires = [ cl-lib ];
         meta = {
@@ -493,10 +493,10 @@
       elpaBuild {
         pname = "company-ebdb";
         ename = "company-ebdb";
-        version = "1";
+        version = "1.1";
         src = fetchurl {
-          url = "https://elpa.gnu.org/packages/company-ebdb-1.el";
+          url = "https://elpa.gnu.org/packages/company-ebdb-1.1.el";
-          sha256 = "1awriwvjpf9k2r6hzawai5kxz28j40zk9fvpb946kd5yj0hxr9nc";
+          sha256 = "146qpiigz12zp1823ggxfrx090g0mxs7gz1ba7sa0iq6ibgzwwm9";
         };
         packageRequires = [ company ebdb ];
         meta = {
@@ -775,10 +775,10 @@
       elpaBuild {
         pname = "djvu";
         ename = "djvu";
-        version = "0.5";
+        version = "1.0.1";
         src = fetchurl {
-          url = "https://elpa.gnu.org/packages/djvu-0.5.el";
+          url = "https://elpa.gnu.org/packages/djvu-1.0.1.el";
-          sha256 = "1wpyv4ismfsz5hfaj75j3h3nni1mnk33czhw3rd45cf32a2zkqsj";
+          sha256 = "1am4cm9csc5df3mbdby7j197j8yxv0x0maf6kfmn2ww1iwcyv8x6";
         };
         packageRequires = [];
         meta = {
@@ -920,10 +920,10 @@
       elpaBuild {
         pname = "el-search";
         ename = "el-search";
-        version = "1.8.7";
+        version = "1.8.8";
         src = fetchurl {
-          url = "https://elpa.gnu.org/packages/el-search-1.8.7.tar";
+          url = "https://elpa.gnu.org/packages/el-search-1.8.8.tar";
-          sha256 = "0jlalcz8hppra2chmppd6b2g5dz8w6yscqylkx28pd7wy6aadx1r";
+          sha256 = "1yv91vzpxn29rr8rkrihcbf26pafnxj25j7g38rss9qigswjkpnk";
         };
         packageRequires = [ cl-print emacs stream ];
         meta = {
@@ -1267,10 +1267,10 @@
       elpaBuild {
         pname = "gpastel";
         ename = "gpastel";
-        version = "0.3.0";
+        version = "0.5.0";
         src = fetchurl {
-          url = "https://elpa.gnu.org/packages/gpastel-0.3.0.el";
+          url = "https://elpa.gnu.org/packages/gpastel-0.5.0.el";
-          sha256 = "0426y55f7mbfbyjhl2bn0c2cn57jd4d8xvzri2pbqakff8ij470a";
+          sha256 = "1wky6047071vgyyw2m929nbwg4d9qqp1mjqwk7a5rs8hfr4xqxfw";
         };
         packageRequires = [ emacs ];
         meta = {
@@ -2013,10 +2013,10 @@
       elpaBuild {
         pname = "org";
         ename = "org";
-        version = "9.1.14";
+        version = "9.2";
         src = fetchurl {
-          url = "https://elpa.gnu.org/packages/org-9.1.14.tar";
+          url = "https://elpa.gnu.org/packages/org-9.2.tar";
-          sha256 = "17vd9hig26rqv90l6y92hc2i0x29g44lsdsp0xd4m53s8r3zdikz";
+          sha256 = "14ydwh2r360fpi6v2g9rgf0zazy2ddq1pcdxvzn73h65glnnclz9";
         };
         packageRequires = [];
         meta = {

pkgs/applications/editors/emacs-modes/melpa-packages.nix

@@ -89,6 +89,12 @@ self:
       # Expects bash to be at /bin/bash
       flycheck-rtags = markBroken super.flycheck-rtags;
 
+      forge = super.forge.overrideAttrs (attrs: {
+        # searches for Git at build time
+        nativeBuildInputs =
+          (attrs.nativeBuildInputs or []) ++ [ external.git ];
+      });
+
       # build timeout
       graphene = markBroken super.graphene;
 

pkgs/applications/editors/emacs-modes/melpa-stable-packages.nix

@@ -35,9 +35,6 @@ self:
     });
 
     overrides = {
-      # upstream issue: mismatched filename
-      ack-menu = markBroken super.ack-menu;
-
       # Expects bash to be at /bin/bash
       ac-rtags = markBroken super.ac-rtags;
 
@@ -102,9 +99,6 @@ self:
       # build timeout
       graphene = markBroken super.graphene;
 
-      # upstream issue: mismatched filename
-      helm-lobsters = markBroken super.helm-lobsters;
-
       # Expects bash to be at /bin/bash
       helm-rtags = markBroken super.helm-rtags;
 
@@ -134,9 +128,6 @@ self:
       # upstream issue: missing file header
       link = markBroken super.link;
 
-      # upstream issue: mismatched filename
-      link-hint = markBroken super.link-hint;
-
       # upstream issue: missing file header
       maxframe = markBroken super.maxframe;
 
@@ -185,9 +176,6 @@ self:
       # upstream issue: truncated file
       powershell = markBroken super.powershell;
 
-      # upstream issue: mismatched filename
-      processing-snippets = markBroken super.processing-snippets;
-
       # upstream issue: missing file header
       qiita = markBroken super.qiita;
 

pkgs/applications/editors/emacs-modes/org-generated.nix

@@ -4,10 +4,10 @@
       elpaBuild {
         pname = "org";
         ename = "org";
-        version = "20181217";
+        version = "20181230";
         src = fetchurl {
-          url = "http://orgmode.org/elpa/org-20181217.tar";
+          url = "http://orgmode.org/elpa/org-20181230.tar";
-          sha256 = "0j301z0429dnk1d3bn7524y848vp9il41sxpm9z9hs7gpzfdcw28";
+          sha256 = "1ydl6cikf4myrz59qvajbdxg1bvbpqjlkxn54qhrhh4755llcfkv";
         };
         packageRequires = [];
         meta = {
@@ -19,10 +19,10 @@
       elpaBuild {
         pname = "org-plus-contrib";
         ename = "org-plus-contrib";
-        version = "20181217";
+        version = "20181230";
         src = fetchurl {
-          url = "http://orgmode.org/elpa/org-plus-contrib-20181217.tar";
+          url = "http://orgmode.org/elpa/org-plus-contrib-20181230.tar";
-          sha256 = "1p7v9246zxkp68kc63550x3w7pmhx1drgj20wmddhvs0bqd3k3ap";
+          sha256 = "0gibwcjlardjwq19bh0zzszv0dxxlml0rh5iikkcdynbgndk1aa1";
         };
         packageRequires = [];
         meta = {

pkgs/applications/editors/neovim/qt.nix

@@ -58,6 +58,10 @@ in
     '' else ''
       makeWrapper '${unwrapped}/bin/nvim-qt' "$out/bin/nvim-qt" \
         --prefix PATH : "${neovim}/bin"
+
+      # link .desktop file
+      mkdir -p "$out/share"
+      ln -s '${unwrapped}/share/applications' "$out/share/applications"
     '';
 
     preferLocalBuild = true;

pkgs/applications/editors/vscode/default.nix

@@ -12,9 +12,9 @@ let
   }.${stdenv.hostPlatform.system};
 
   sha256 = {
-    "i686-linux" = "1xadkgqfwsl53blm2f0kdvczwmag47585dswa1hpafzc8i86009b";
+    "i686-linux" = "1g73fay6fxlqhalkqq5m6rjbp68k9npk0rrxrkhdj8mw0cz74dpm";
-    "x86_64-linux" = "0h77kc6z9c5bkkb8svjxjabnbbv0lb835kzd1c2yypamkhag9j4a";
+    "x86_64-linux" = "0mil8n5i2ajdyrgq862wq59ajy2122rvvn7m7mxq4ab92sk26rix";
-    "x86_64-darwin" = "1f8grgav5capd2mm1nx0416na8c6qjh91680cfvf1jh4pjihs6g4";
+    "x86_64-darwin" = "07r52scs1sgafzxqal39r8vf9p9qqvwwx8f6z09gqcf6clr6k48q";
   }.${stdenv.hostPlatform.system};
 
   archive_fmt = if stdenv.hostPlatform.system == "x86_64-darwin" then "zip" else "tar.gz";
@@ -31,7 +31,7 @@ let
 in
   stdenv.mkDerivation rec {
     name = "vscode-${version}";
-    version = "1.30.1";
+    version = "1.30.2";
 
     src = fetchurl {
       name = "VSCode_${version}_${plat}.${archive_fmt}";

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

@@ -14,10 +14,10 @@ rec {
 
   firefox = common rec {
     pname = "firefox";
-    ffversion = "64.0";
+    ffversion = "64.0.2";
     src = fetchurl {
       url = "mirror://mozilla/firefox/releases/${ffversion}/source/firefox-${ffversion}.source.tar.xz";
-      sha512 = "10zbzwpdadj3ap2z66d0bz8l11qkgzlzd22nj7n3k2bzy7rd0m6cfznd9d4mgyl4ivxjv6wz8pasvacrala2dr0m78ysxiz2fpvrahs";
+      sha512 = "2xvzbx20i2qwld04g3wl9j6j8bkcja3i83sf9cpngayllhrjki29020izrwjxrgm0z3isg7zijw656v1v2zzmhlfkpkbk71n2gjj7md";
     };
 
     patches = nixpkgsPatches ++ [

pkgs/applications/networking/cluster/openshift/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchFromGitHub, removeReferencesTo, which, go, go-bindata, makeWrapper, rsync, utillinux
+{ stdenv, lib, fetchFromGitHub, buildGoPackage, which, go-bindata, rsync, utillinux
 , coreutils, kerberos, clang
 , components ? [
   "cmd/oc"
@@ -20,7 +20,7 @@ let
   k8sgitcommit = "b1b2997";
   k8sgitMajor = "0";
   k8sgitMinor = "1";
-in stdenv.mkDerivation rec {
+in buildGoPackage rec {
   name = "openshift-origin-${version}";
   inherit version;
 
@@ -29,13 +29,13 @@ in stdenv.mkDerivation rec {
     repo = "origin";
     rev = "v${version}";
     sha256 = "06q4v2a1mm6c659ab0rzkqz6b66vx4avqfg0s9xckwhq420lzgka";
-};
+  };
+
+  goPackagePath = "github.com/openshift/origin";
 
   # go > 1.10
   # [FATAL] [14:44:02+0000] Please install Go version go or use PERMISSIVE_GO=y to bypass this check.
-  buildInputs = [ removeReferencesTo makeWrapper which go rsync go-bindata kerberos clang ];
+  buildInputs = [ which rsync go-bindata kerberos clang ];
-
-  outputs = [ "out" ];
 
   patchPhase = ''
     patchShebangs ./hack
@@ -54,6 +54,7 @@ in stdenv.mkDerivation rec {
   '';
 
   buildPhase = ''
+    cd go/src/${goPackagePath}
     # Openshift build require this variables to be set
     # unless there is a .git folder which is not the case with fetchFromGitHub
     echo "OS_GIT_VERSION=v${version}" >> os-version-defs
@@ -71,14 +72,10 @@ in stdenv.mkDerivation rec {
   '';
 
   installPhase = ''
-    mkdir -p "$out/bin"
+    mkdir -p $bin/bin
-    cp -a "_output/local/bin/$(go env GOOS)/$(go env GOARCH)/"* "$out/bin/"
+    cp -a "_output/local/bin/$(go env GOOS)/$(go env GOARCH)/"* "$bin/bin/"
-    install -D -t "$out/etc/bash_completion.d" contrib/completions/bash/*
+    install -D -t "$bin/etc/bash_completion.d" contrib/completions/bash/*
-    install -D -t "$out/share/zsh/site-functions" contrib/completions/zsh/*
+    install -D -t "$bin/share/zsh/site-functions" contrib/completions/zsh/*
-  '';
-
-  preFixup = ''
-    find $out/bin -type f -exec remove-references-to -t ${go} '{}' +
   '';
 
   meta = with stdenv.lib; {

pkgs/applications/networking/flexget/default.nix

@@ -55,6 +55,8 @@ buildPythonApplication rec {
     pyparsing zxcvbn-python future
     # Optional requirements
     deluge-client
+    # Plugins
+    transmissionrpc
   ] ++ lib.optional (pythonOlder "3.4") pathlib;
 
   meta = with lib; {

pkgs/applications/networking/gns3/server.nix

@@ -1,63 +1,54 @@
 { stable, branch, version, sha256Hash }:
 
-{ stdenv, python36Packages, fetchFromGitHub, fetchurl }:
+{ stdenv, python36, fetchFromGitHub }:
 
 let
-  pythonPackages = python36Packages;
+  python = python36.override {
-  async-timeout = pythonPackages.async-timeout.overrideAttrs
+    packageOverrides = self: super: {
-    (oldAttrs:
+      async-timeout = super.async-timeout.overridePythonAttrs (oldAttrs: rec {
-      rec {
-        pname = "async-timeout";
         version = "2.0.1";
-        src = pythonPackages.fetchPypi {
+        src = oldAttrs.src.override {
-          inherit pname version;
+          inherit version;
           sha256 = "1l3kg062m02mph6rf9rdv8r5c5n356clxa6b6mrn0i77vk9g9kq0";
         };
       });
-  aiohttp = pythonPackages.aiohttp.overrideAttrs
+      aiohttp = super.aiohttp.overridePythonAttrs (oldAttrs: rec {
-    (oldAttrs:
-      rec {
-        pname = "aiohttp";
         version = "2.3.10";
-        src = pythonPackages.fetchPypi {
+        src = oldAttrs.src.override {
-          inherit pname version;
+          inherit version;
           sha256 = "8adda6583ba438a4c70693374e10b60168663ffa6564c5c75d3c7a9055290964";
         };
-        propagatedBuildInputs = [ async-timeout ]
+        propagatedBuildInputs = with self; [ async-timeout attrs chardet multidict yarl idna-ssl ];
-          ++ (with pythonPackages; [ attrs chardet multidict yarl idna-ssl ]);
+        doCheck = false;
       });
-  aiohttp-cors = pythonPackages.aiohttp-cors.overrideAttrs
+      aiohttp-cors = super.aiohttp-cors.overridePythonAttrs (oldAttrs: rec {
-    (oldAttrs:
-      rec {
-        pname = "aiohttp-cors";
         version = "0.5.3";
-        name = "${pname}-${version}";
+        src = oldAttrs.src.override {
-        src = pythonPackages.fetchPypi {
+          inherit version;
-          inherit pname version;
           sha256 = "11b51mhr7wjfiikvj3nc5s8c7miin2zdhl3yrzcga4mbpkj892in";
         };
-        propagatedBuildInputs = [ aiohttp ]
+        propagatedBuildInputs = with self; [ aiohttp ]
-          ++ stdenv.lib.optional
+          ++ stdenv.lib.optional (pythonOlder "3.5") typing;
-               (pythonPackages.pythonOlder "3.5")
-               pythonPackages.typing;
       });
-in pythonPackages.buildPythonPackage rec {
+    };
-  name = "${pname}-${version}";
+  };
+
+in python.pkgs.buildPythonPackage {
   pname = "gns3-server";
+  inherit version;
 
   src = fetchFromGitHub {
     owner = "GNS3";
-    repo = pname;
+    repo = "gns3-server";
     rev = "v${version}";
     sha256 = sha256Hash;
   };
 
-  propagatedBuildInputs = [ aiohttp-cors ]
+  propagatedBuildInputs = with python.pkgs; [
-    ++ (with pythonPackages; [
+    aiohttp-cors yarl aiohttp multidict
-      yarl aiohttp multidict
+    jinja2 psutil zipstream raven jsonschema typing
-      jinja2 psutil zipstream raven jsonschema typing
+    (python.pkgs.callPackage ../../../development/python-modules/prompt_toolkit/1.nix {})
-      (pythonPackages.callPackage ../../../development/python-modules/prompt_toolkit/1.nix {})
+  ];
-    ]);
 
   # Requires network access
   doCheck = false;
@@ -65,6 +56,7 @@ in pythonPackages.buildPythonPackage rec {
   postInstall = ''
     rm $out/bin/gns3loopback # For Windows only
   '';
+
   meta = with stdenv.lib; {
     description = "Graphical Network Simulator 3 server (${branch} release)";
     longDescription = ''

pkgs/applications/networking/mailreaders/claws-mail/default.nix

@@ -31,11 +31,11 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "claws-mail-${version}";
-  version = "3.17.2";
+  version = "3.17.3";
 
   src = fetchurl {
     url = "http://www.claws-mail.org/download.php?file=releases/claws-mail-${version}.tar.xz";
-    sha256 = "1hb17kpvfl8f1y49zan0wvf4awapxg13bqbqwrbhq2n4xp445kr5";
+    sha256 = "1wnj6c9cbmhphs2l6wfvndkk2g08rmxw0sl2c8k1k008dxd1ykjh";
   };
 
   outputs = [ "out" "dev" ];

pkgs/applications/networking/omping/default.nix

@@ -0,0 +1,35 @@
+{ stdenv, fetchFromGitHub, fetchpatch }:
+
+stdenv.mkDerivation rec {
+  name = "omping-${version}";
+  version = "0.0.5";
+
+  src = fetchFromGitHub {
+    owner  = "troglobit";
+    repo   = "omping";
+    rev    = version;
+    sha256 = "1f0vsbnhxp7bbgdnfqshryx3nhz2sqdnxdj068s0nmzsh53ckbf7";
+  };
+
+  patches = [
+    # This can go in 0.0.6+
+    (fetchpatch {
+      url    = "https://github.com/troglobit/omping/commit/08a31ec1a6eb4e8f88c301ef679c3b6f9893f333.patch";
+      sha256 = "1xafyvd46bq53w2zvjw8bdw7vjqbrcrr21cyh6d0zfcn4gif1k0f";
+      name   = "fix_manpage_install.patch";
+    })
+  ];
+
+  makeFlags = [
+    "PREFIX=${placeholder "out"}"
+  ];
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    description = "Open Multicast Ping (omping) is a tool for testing IPv4/IPv6 multicast connectivity on a LAN.";
+    license = licenses.mit;
+    platforms = platforms.unix;
+    inherit (src.meta) homepage;
+  };
+}

pkgs/applications/networking/p2p/transmission-remote-gtk/default.nix

@@ -5,13 +5,13 @@
 
 stdenv.mkDerivation rec {
   name = "transmission-remote-gtk-${version}";
-  version = "1.4.0";
+  version = "1.4.1";
 
   src = fetchFromGitHub {
     owner = "transmission-remote-gtk";
     repo = "transmission-remote-gtk";
     rev = "${version}";
-    sha256 = "126s7aqh9j06zvnwhjbql5x9ibz05pdrrzwb9c6h4qndvr8iqqff";
+    sha256 = "1pipc1f94jdppv597mqmcj2kw2rdvaqcbl512v7z8vir76p1a7gk";
   };
 
   preConfigure = "./autogen.sh";

pkgs/applications/science/biology/bftools/default.nix

@@ -0,0 +1,41 @@
+{ stdenv, lib, makeWrapper, fetchzip, jre }:
+
+stdenv.mkDerivation rec {
+  name = "bftools-${version}";
+  version = "5.9.2";
+
+  src = fetchzip {
+    url = "http://downloads.openmicroscopy.org/bio-formats/${version}/artifacts/bftools.zip";
+    sha256 = "08lmbg3kfxh17q6548il0i2h3f9a6ch8r0r067p14dajhzfpjyqj";
+  };
+
+  installPhase = ''
+    find . -maxdepth 1 -perm -111 -type f -not -name "*.sh" \
+      -exec install -vD {} "$out"/bin/{} \;
+
+    mkdir $out/libexec
+    mkdir -p $out/share/java
+
+    cp ./*.sh $out/libexec
+    cp ./*.jar $out/share/java
+
+    for file in $out/bin/*; do
+      substituteInPlace $file --replace "\$BF_DIR" $out/libexec
+    done
+    substituteInPlace $out/libexec/bf.sh --replace "\$BF_JAR_DIR" $out/share/java
+  '';
+
+  postFixup = ''
+    wrapProgram $out/libexec/bf.sh --prefix PATH : "${lib.makeBinPath [ jre ]}"
+  '';
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  meta = with stdenv.lib; {
+    description = "A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included";
+    license = licenses.gpl2;
+    platforms = platforms.all;
+    homepage = https://www.openmicroscopy.org/bio-formats/;
+    maintainers = [ maintainers.tbenst ];
+  };
+}

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

@@ -1,12 +1,13 @@
 {stdenv, fetchurl, bison, flex
 , readline, libX11, libICE, libXaw, libXmu, libXext, libXt, fftw }:
 
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
-  name = "ngspice-29";
+  name = "ngspice-${version}";
+  version = "30";
 
   src = fetchurl {
-    url = "mirror://sourceforge/ngspice/ngspice-29.tar.gz";
+    url = "mirror://sourceforge/ngspice/ngspice-${version}.tar.gz";
-    sha256 = "0jjwz73naq7l9yhwdqbpnrfckywp2ffkppivxjv8w92zq7xhyvcd";
+    sha256 = "15v0jdfy2a2zxp8dmy04fdp7w7a4vwvffcwa688r81b86wphxzh8";
   };
 
   nativeBuildInputs = [ flex bison ];

pkgs/applications/science/misc/root/5.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchurl, cmake, pcre, pkgconfig, python2
 , libX11, libXpm, libXft, libXext, libGLU_combined, zlib, libxml2, lzma, gsl_1
-, Cocoa, OpenGL, noSplash ? false }:
+, Cocoa, OpenGL, cf-private, noSplash ? false }:
 
 stdenv.mkDerivation rec {
   name = "root-${version}";
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ cmake pcre python2 zlib libxml2 lzma gsl_1 ]
     ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU_combined ]
-    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
+    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL cf-private ]
     ;
 
   patches = [
@@ -73,5 +73,8 @@ stdenv.mkDerivation rec {
     description = "A data analysis framework";
     platforms = platforms.unix;
     maintainers = with maintainers; [ veprbl ];
+    # needs to be adapted to work with modern glibc
+    # it works on darwin by impurely picking up system's libc headers
+    broken = stdenv.isLinux;
   };
 }

pkgs/applications/science/misc/root/default.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchurl, cmake, pcre, pkgconfig, python2
 , libX11, libXpm, libXft, libXext, libGLU_combined, zlib, libxml2, lz4, lzma, gsl, xxHash
-, Cocoa, OpenGL, noSplash ? false }:
+, Cocoa, OpenGL, cf-private, noSplash ? false }:
 
 stdenv.mkDerivation rec {
   name = "root-${version}";
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ cmake pcre python2 zlib libxml2 lz4 lzma gsl xxHash ]
     ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU_combined ]
-    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
+    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL cf-private ]
     ;
 
   patches = [

pkgs/applications/version-management/git-and-tools/grv/default.nix

@@ -1,11 +1,11 @@
-{ stdenv, buildGo19Package, fetchFromGitHub, curl, libgit2, ncurses, pkgconfig, readline }:
+{ stdenv, buildGo19Package, fetchFromGitHub, curl, libgit2_0_27, ncurses, pkgconfig, readline }:
 let
   version = "0.3.1";
 in
 buildGo19Package {
   name = "grv-${version}";
 
-  buildInputs = [ ncurses readline curl libgit2 ];
+  buildInputs = [ ncurses readline curl libgit2_0_27 ];
   nativeBuildInputs = [ pkgconfig ];
 
   goPackagePath = "github.com/rgburke/grv";

pkgs/applications/video/handbrake/default.nix

@@ -1,72 +1,64 @@
 # Upstream distributes HandBrake with bundle of according versions of libraries and patches to them.
 #
-# Derivation patches HandBrake to use our closure.
+# Derivation patches HandBrake to use Nix closure dependencies.
 #
 
-{ stdenv, lib, fetchurl,
+{ stdenv, lib, fetchurl, callPackage,
-  python2, pkgconfig, yasm, zlib,
+  # Main build tools
-  autoconf, automake, libtool, m4, jansson,
+  python2, pkgconfig, autoconf, automake, cmake, nasm, libtool, m4,
-  libass, libiconv, libsamplerate, fribidi, libxml2, bzip2,
+  # Processing, video codecs, containers
-  libogg, libopus, libtheora, libvorbis, libdvdcss, a52dec,
+  ffmpeg-full, nv-codec-headers, libogg, x264, x265, libvpx, libtheora,
-  lame, libdvdread, libdvdnav, libbluray,
+  # Codecs, audio
-  mp4v2, mpeg2dec, x264, x265, libmkv,
+  libopus, lame, libvorbis, a52dec, speex, libsamplerate,
-  fontconfig, freetype, hicolor-icon-theme,
+  # Text processing
-  glib, gtk3, intltool, libnotify,
+  libiconv, fribidi, fontconfig, freetype, libass, jansson, libxml2,
-  gst_all_1, dbus-glib, udev, libgudev, libvpx,
+  # Optical media
-  useGtk ? true, wrapGAppsHook ? null, libappindicator-gtk3 ? null,
+  libdvdread, libdvdnav, libdvdcss, libbluray,
-  useFfmpeg ? false, libav_12 ? null, ffmpeg ? null,
+  useGtk ? true, wrapGAppsHook ? null,
+                 intltool ? null,
+                 glib ? null,
+                 gtk3 ? null,
+                 libappindicator-gtk3 ? null,
+                 libnotify ? null,
+                 gst_all_1 ? null,
+                 dbus-glib ? null,
+                 udev ? null,
+                 libgudev ? null,
+                 hicolor-icon-theme ? null,
   useFdk ? false, fdk_aac ? null
 }:
 
 stdenv.mkDerivation rec {
-  # TODO: Release 1.2.0 would switch LibAV to FFmpeg.
+  version = "1.2.0";
-  version = "1.1.2";
   name = "handbrake-${version}";
 
   src = fetchurl {
     url = ''https://download2.handbrake.fr/${version}/HandBrake-${version}-source.tar.bz2'';
-    sha256 = "0bny0hwlr55g2c69rsamv0xvwmfh1s4a582b9vq20xv5ly84m6ms";
+    sha256 = "03clkknaq3mz84p85cvr21gsy9b8vv2g4vvyfz44hz8la253jfqi";
   };
 
-  patched_libav_12 = libav_12.overrideAttrs (super: {
-    patches = (super.patches or []) ++ [(
-      # NOTE: 2018-04-26: HandBrake compilation (1.1.0) requires
-      # a patch of LibAV (12.3) from HandBrake team. This patch
-      # not went LibAV upstream.
-      fetchurl {
-        url = ''https://raw.githubusercontent.com/HandBrake/HandBrake/9e1f245708a157231c427c0ef9b91729d59a30e1/contrib/ffmpeg/A21-mp4-sdtp.patch'';
-        sha256 = "14grzyvb1qbb90k31ibabnwmwnrc48ml6h2z0rjamdv83q45jq4g";
-      })
-      # NOTE: 2018-11-11: Transcoding to MP4 can fail with:
-      #
-      # Tag avc1/0x31637661 incompatible with output codec id '28'
-      # muxavformat: avformat_write_header failed!
-      #
-      # Fix using Handbrake patch that is not upstream in libav.
-      (
-      fetchurl {
-        url = ''https://raw.githubusercontent.com/HandBrake/HandBrake/df6c26fa261423237ee2bec0bf784c32cbfda3fa/contrib/ffmpeg/A20-avc3-hvc1-override.patch'';
-        sha256 = "1vijd7bmkzp3sb6zhpcpdni8fz4h13wgglnml6cz9f44j41w2c3v";
-      })
-    ];
-  });
-
   nativeBuildInputs = [
-    python2 pkgconfig yasm autoconf automake libtool m4
+    python2 pkgconfig autoconf automake cmake nasm libtool m4
   ] ++ lib.optionals useGtk [ intltool wrapGAppsHook ];
 
   buildInputs = [
-    fribidi fontconfig freetype jansson zlib
+    ffmpeg-full libogg libtheora x264 x265 libvpx
-    libass libiconv libsamplerate libxml2 bzip2
+    libopus lame libvorbis a52dec speex libsamplerate
-    libogg libopus libtheora libvorbis libdvdcss a52dec libmkv
+    libiconv fribidi fontconfig freetype libass jansson libxml2
-    lame libdvdread libdvdnav libbluray mp4v2 mpeg2dec x264 x265 libvpx
+    libdvdread libdvdnav libdvdcss libbluray
   ] ++ lib.optionals useGtk [
     glib gtk3 libappindicator-gtk3 libnotify
     gst_all_1.gstreamer gst_all_1.gst-plugins-base dbus-glib udev
     libgudev hicolor-icon-theme
-  ] ++ (if useFfmpeg then [ ffmpeg ] else [ patched_libav_12 ])
+  ] ++ lib.optional useFdk fdk_aac
-  ++ lib.optional useFdk fdk_aac;
+  # NOTE: 2018-12-27: Handbrake supports nv-codec-headers for Linux only,
+  # look at ./make/configure.py search "enable_nvenc"
+    ++ lib.optional stdenv.isLinux nv-codec-headers;
 
+  # NOTE: 2018-12-25: v1.2.0 now requires cmake dep
+  # (default distribution bundles&builds 3rd party libs),
+  # don't trigger cmake build
+  dontUseCmakeConfigure = true;
   enableParallelBuilding = true;
 
   preConfigure = ''
@@ -87,6 +79,7 @@ stdenv.mkDerivation rec {
     (if useFdk then "--enable-fdk-aac"            else "")
   ];
 
+  # NOTE: 2018-12-27: Check NixOS HandBrake test if changing
   NIX_LDFLAGS = [
     "-lx265"
   ];

pkgs/applications/video/obs-studio/default.nix

@@ -21,6 +21,11 @@
 , vlc
 , mbedtls
 
+, scriptingSupport ? true
+, luajit
+, swig
+, python3
+
 , alsaSupport ? false
 , alsaLib
 , pulseaudioSupport ? false
@@ -68,6 +73,7 @@ in stdenv.mkDerivation rec {
                   makeWrapper
                   mbedtls
                 ]
+                ++ optional scriptingSupport [ luajit swig python3 ]
                 ++ optional alsaSupport alsaLib
                 ++ optional pulseaudioSupport libpulseaudio;
 

pkgs/applications/video/qmediathekview/default.nix

@@ -2,14 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "QMediathekView";
-  version = "2017-04-16";
+  version = "2019-01-06";
-  name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "adamreichold";
     repo = pname;
-    rev = "8c69892b95bf6825bd06a8c594168a98fe7cb2d1";
+    rev = "e098aaec552ec4e367078bf19953a08067316b4b";
-    sha256 = "1wca1w4iywd3hmiwcqx6fv79p3x5n1cgbw2liw3hs24ch3z54ckm";
+    sha256 = "0i9hac9alaajbra3lx23m0iiq6ww4is00lpbzg5x70agjrwj0nd6";
   };
 
   postPatch = ''

pkgs/applications/virtualization/containerd/default.nix

@@ -1,9 +1,8 @@
-{ stdenv, lib, fetchFromGitHub, removeReferencesTo
+{ stdenv, lib, fetchFromGitHub, buildGoPackage, btrfs-progs, go-md2man, utillinux }:
-, go, btrfs-progs }:
 
 with lib;
 
-stdenv.mkDerivation rec {
+buildGoPackage rec {
   name = "containerd-${version}";
   version = "1.2.1";
 
@@ -14,34 +13,37 @@ stdenv.mkDerivation rec {
     sha256 = "16zn6p1ky3yrgn53z8h9wza53ch91fj47wj5xgz6w4c57j30f66p";
   };
 
+  goPackagePath = "github.com/containerd/containerd";
+  outputs = [ "bin" "out" "man" ];
+
   hardeningDisable = [ "fortify" ];
 
-  buildInputs = [ removeReferencesTo go btrfs-progs ];
+  buildInputs = [ btrfs-progs go-md2man utillinux ];
   buildFlags = "VERSION=v${version}";
 
   BUILDTAGS = []
     ++ optional (btrfs-progs == null) "no_btrfs";
 
-  preConfigure = ''
+  buildPhase = ''
-    # Extract the source
+    cd go/src/${goPackagePath}
-    cd "$NIX_BUILD_TOP"
-    mkdir -p "go/src/github.com/containerd"
-    mv "$sourceRoot" "go/src/github.com/containerd/containerd"
-    export GOPATH=$NIX_BUILD_TOP/go:$GOPATH
-'';
-
-  preBuild = ''
-    cd go/src/github.com/containerd/containerd
     patchShebangs .
+    make binaries
   '';
 
   installPhase = ''
-    mkdir -p $out/bin
+    for b in bin/*; do
-    cp bin/* $out/bin
+      install -Dm555 $b $bin/$b
-  '';
+    done
 
-  preFixup = ''
+    make man
-    find $out -type f -exec remove-references-to -t ${go} '{}' +
+    manRoot="$man/share/man"
+    mkdir -p "$manRoot"
+    for manFile in man/*; do
+      manName="$(basename "$manFile")" # "docker-build.1"
+      number="$(echo $manName | rev | cut -d'.' -f1 | rev)"
+      mkdir -p "$manRoot/man$number"
+      gzip -c "$manFile" > "$manRoot/man$number/$manName.gz"
+    done
   '';
 
   meta = {

pkgs/applications/virtualization/docker/default.nix

@@ -28,7 +28,7 @@ rec {
       patches = [];
     });
 
-    docker-containerd = (containerd.override { inherit go; }).overrideAttrs (oldAttrs: rec {
+    docker-containerd = containerd.overrideAttrs (oldAttrs: rec {
       name = "docker-containerd-${version}";
       inherit version;
       src = fetchFromGitHub {
@@ -39,8 +39,6 @@ rec {
       };
 
       hardeningDisable = [ "fortify" ];
-
-      buildInputs = [ removeReferencesTo go btrfs-progs ];
     });
 
     docker-tini = tini.overrideAttrs  (oldAttrs: rec {

pkgs/build-support/docker/default.nix

@@ -316,14 +316,21 @@ rec {
     # Files to add to the layer.
     contents,
     baseJson,
+    extraCommands,
     uid ? 0, gid ? 0,
   }:
     runCommand "${name}-customisation-layer" {
       buildInputs = [ jshon rsync tarsum ];
+      inherit extraCommands;
     }
     ''
       cp -r ${contents}/ ./layer
 
+      if [[ -n $extraCommands ]]; then
+        chmod ug+w layer
+        (cd layer; eval "$extraCommands")
+      fi
+
       # Tar up the layer and throw it into 'layer.tar'.
       echo "Packing layer..."
       mkdir $out
@@ -494,6 +501,8 @@ rec {
     # Time of creation of the image. Passing "now" will make the
     # created date be the time of building.
     created ? "1970-01-01T00:00:01Z",
+    # Optional bash script to run on the files prior to fixturizing the layer.
+    extraCommands ? "", uid ? 0, gid ? 0,
     # Docker's lowest maximum layer limit is 42-layers for an old
     # version of the AUFS graph driver. We pick 24 to ensure there is
     # plenty of room for extension. I believe the actual maximum is
@@ -501,8 +510,6 @@ rec {
     maxLayers ? 24
   }:
     let
-      uid = 0;
-      gid = 0;
       baseName = baseNameOf name;
       contentsEnv = symlinkJoin { name = "bulk-layers"; paths = (if builtins.isList contents then contents else [ contents ]); };
 
@@ -531,7 +538,7 @@ rec {
           name = baseName;
           contents = contentsEnv;
           baseJson = configJson;
-          inherit uid gid;
+          inherit uid gid extraCommands;
         };
       result = runCommand "docker-image-${baseName}.tar.gz" {
         buildInputs = [ jshon pigz coreutils findutils jq ];

pkgs/build-support/docker/examples.nix

@@ -155,6 +155,7 @@ rec {
   layered-image = pkgs.dockerTools.buildLayeredImage {
     name = "layered-image";
     tag = "latest";
+    extraCommands = ''echo "(extraCommand)" > extraCommands'';
     config.Cmd = [ "${pkgs.hello}/bin/hello" ];
     contents = [ pkgs.hello pkgs.bash pkgs.coreutils ];
   };

pkgs/data/fonts/culmus/default.nix

@@ -2,19 +2,24 @@
 
 let
   version = "0.133";
-in fetchzip {
+in stdenv.mkDerivation {
   name = "culmus-${version}";
 
-  url = "mirror://sourceforge/culmus/culmus/${version}/culmus-${version}.tar.gz";
+  src = fetchzip {
+    url = "mirror://sourceforge/culmus/culmus/${version}/culmus-${version}.tar.gz";
+    sha256 = "0q80j3vixn364sc23hcy6098rkgy0kb4p91lky6224am1dwn2qmr";
+  };
 
-  postFetch = ''
+  installPhase = ''
-    tar -xzvf $downloadedFile --strip-components=1
+    mkdir -p $out/share/fonts/{truetype,type1}
-    mkdir -p $out/share/fonts/truetype
+    cp -v *.pfa $out/share/fonts/type1/
+    cp -v *.afm $out/share/fonts/type1/
+    cp -v fonts.scale-type1 $out/share/fonts/type1/fonts.scale
     cp -v *.ttf $out/share/fonts/truetype/
+    cp -v *.otf $out/share/fonts/truetype/
+    cp -v fonts.scale-ttf $out/share/fonts/truetype/fonts.scale
   '';
 
-  sha256 = "1jxg2wf4kwasp5cia00nki2lrcdnhsyh4yy7d05l0a9bim5hq2lr";
-
   meta = {
     description = "Culmus Hebrew fonts";
     longDescription = "The Culmus project aims at providing the Hebrew-speaking GNU/Linux and Unix community with a basic collection of Hebrew fonts for X Windows.";

pkgs/desktops/gnome-3/core/gnome-system-log/default.nix

@@ -1,35 +0,0 @@
-{ stdenv, intltool, fetchurl, pkgconfig
-, gtk3, glib, wrapGAppsHook
-, itstool, gnome3, libxml2 }:
-
-let
-  pname = "gnome-system-log";
-  version = "3.9.90";
-in stdenv.mkDerivation rec {
-  name = "${pname}-${version}";
-
-  src = fetchurl {
-    url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${name}.tar.xz";
-    sha256 = "9eeb51982d347aa7b33703031e2c1d8084201374665425cd62199649b29a5411";
-  };
-
-  doCheck = true;
-
-  nativeBuildInputs = [ pkgconfig intltool itstool wrapGAppsHook libxml2 ];
-  buildInputs = [ gtk3 glib gnome3.gsettings-desktop-schemas gnome3.defaultIconTheme ];
-
-  passthru = {
-    updateScript = gnome3.updateScript {
-      packageName = pname;
-      attrPath = "gnome3.${pname}";
-      versionPolicy = "none";
-    };
-  };
-
-  meta = with stdenv.lib; {
-    description = "Graphical, menu-driven viewer that you can use to view and monitor your system logs";
-    maintainers = gnome3.maintainers;
-    license = licenses.gpl2;
-    platforms = platforms.linux;
-  };
-}

pkgs/desktops/gnome-3/default.nix

@@ -19,7 +19,7 @@ lib.makeScope pkgs.newScope (self: with self; {
   optionalPackages = with gnome3; [ baobab eog epiphany evince
     gucharmap nautilus totem vino yelp gnome-bluetooth
     gnome-calculator gnome-contacts gnome-font-viewer gnome-screenshot
-    gnome-system-log gnome-system-monitor simple-scan
+    gnome-system-monitor simple-scan
     gnome-terminal gnome-user-docs evolution file-roller gedit
     gnome-clocks gnome-music gnome-tweaks gnome-photos
     nautilus-sendto dconf-editor vinagre gnome-weather gnome-logs
@@ -126,8 +126,6 @@ lib.makeScope pkgs.newScope (self: with self; {
 
   gnome-software = callPackage ./core/gnome-software { };
 
-  gnome-system-log = callPackage ./core/gnome-system-log { };
-
   gnome-system-monitor = callPackage ./core/gnome-system-monitor { };
 
   gnome-terminal = callPackage ./core/gnome-terminal { };

pkgs/development/compilers/clasp/default.nix

@@ -1,54 +1,131 @@
-{ stdenv, fetchFromGitHub
+{ stdenv, fetchFromGitHub, fetchFromGitLab
 , llvmPackages
-, cmake, boehmgc, gmp, zlib, ncurses, boost
+, cmake, boehmgc, gmp, zlib, ncurses, boost, libelf
 , python, git, sbcl
 , wafHook
 }:
+let
+  sicl = fetchFromGitHub {
+    owner = "Bike";
+    repo = "SICL";
+    rev = "78052fb5f02a3814eb7295f3dcac09f21f98702b";
+    sha256 = "0wnmp40310ls6q9gkr5ysfkj2qirq26ljjicnkqifc53mm0ghz4i";
+  };
+  cst = fetchFromGitHub {
+    owner = "robert-strandh";
+    repo = "Concrete-Syntax-Tree";
+    rev = "8d8c5abf8f1690cb2b765241d81c2eb86d60d77e";
+    sha256 = "1rs8a5nbfffdyli126sccd0z1a8h5axp222b4pgwvgfxsb9w7g3s";
+  };
+  c2mop = fetchFromGitHub {
+    owner = "pcostanza";
+    repo = "closer-mop";
+    rev = "d4d1c7aa6aba9b4ac8b7bb78ff4902a52126633f";
+    sha256 = "1amcv0f3vbsq0aqhai7ki5bi367giway1pbfxyc47r7q3hq5hw3c";
+  };
+  acclimation = fetchFromGitHub {
+    owner = "robert-strandh";
+    repo = "Acclimation";
+    rev = "dd15c86b0866fc5d8b474be0da15c58a3c04c45c";
+    sha256 = "0ql224qs3zgflvdhfbca621v3byhhqfb71kzy70bslyczxv1bsh2";
+  };
+  eclector = fetchFromGitHub {
+    owner = "robert-strandh";
+    repo = "Eclector";
+    rev = "287ce817c0478668bd389051d2cc6b26ddc62ec9";
+    sha256 = "0v7mgkq49ddyx5vvsradcp772y5l7cv9xrll3280hyginpm8w6q3";
+  };
+  alexandria = fetchFromGitHub {
+    owner = "clasp-developers";
+    repo = "alexandria";
+    rev = "e5c54bc30b0887c237bde2827036d17315f88737";
+    sha256 = "14h7a9fwimiw9gqxjm2h47d95bfhrm7b81f6si7x8vy18d78fn4g";
+  };
+  mps = fetchFromGitHub {
+    owner = "Ravenbrook";
+    repo = "mps";
+    rev = "b8a05a3846430bc36c8200f24d248c8293801503";
+    sha256 = "1q2xqdw832jrp0w9yhgr8xihria01j4z132ac16lr9ssqznkprv6";
+  };
+  asdf = fetchFromGitLab {
+    domain = "gitlab.common-lisp.net";
+    owner = "asdf";
+    repo = "asdf";
+    rev = "3.3.1.2";
+    sha256 = "0ljr2vc0cb2wrijcyjmp9hcaj2bdhh05ci3zf4f43hdq6i2fgg6g";
+  };
+in
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "clasp";
-  version = "0.4.99.20170801";
+  version = "0.8.99.20181128";
 
   src = fetchFromGitHub {
     owner = "drmeister";
     repo = "clasp";
-    rev = "525ce1cffff39311e3e7df6d0b71fa267779bdf5";
+    rev = "2f2b52ccb750048460562b5987a7eaf7a1aa4445";
-    sha256 = "1jqya04wybgxnski341p5sycy2gysxad0s5q8d59z0f6ckj3v8k1";
+    sha256 = "0ra55vdnk59lygwzlxr5cg16vb9c45fmg59wahaxclwm461w7fwz";
     fetchSubmodules = true;
   };
 
-  nativeBuildInputs = [ cmake python git sbcl wafHook ];
+  nativeBuildInputs = [ cmake python git sbcl wafHook ] ++
+    (with llvmPackages; [ llvm clang ]);
 
-  buildInputs = with llvmPackages; (
+  buildInputs = with llvmPackages;
-    builtins.map (x: stdenv.lib.overrideDerivation x
+  (
-         (x: {NIX_CFLAGS_COMPILE= (x.NIX_CFLAGS_COMPILE or "") + " -frtti"; }))
+   builtins.map (x: stdenv.lib.overrideDerivation x
-      [ llvm clang clang-unwrapped clang ]) ++
+           (x: {NIX_CFLAGS_COMPILE= (x.NIX_CFLAGS_COMPILE or "") + " -frtti"; }))
+   [ llvm clang clang-unwrapped clang ]) ++
   [
     gmp zlib ncurses
-    boost boehmgc
+    boost boehmgc libelf
     (boost.override {enableStatic = true; enableShared = false;})
     (stdenv.lib.overrideDerivation boehmgc
       (x: {configureFlags = (x.configureFlags or []) ++ ["--enable-static"];}))
   ];
 
-  NIX_CFLAGS_COMPILE = " -frtti ";
+  NIX_CXXSTDLIB_COMPILE = " -frtti ";
 
   postPatch = ''
     echo "
-      INSTALL_PATH_PREFIX = '$out'
+      PREFIX = '$out'
     " | sed -e 's/^ *//' > wscript.config
+
+    mkdir -p src/lisp/kernel/contrib/sicl
+    mkdir -p src/lisp/kernel/contrib/Concrete-Syntax-Tree
+    mkdir -p src/lisp/kernel/contrib/closer-mop
+    mkdir -p src/lisp/kernel/contrib/Acclimation
+    mkdir -p src/lisp/kernel/contrib/Eclector
+    mkdir -p src/lisp/kernel/contrib/alexandria
+    mkdir -p src/mps
+    mkdir -p src/lisp/modules/asdf
+
+    cp -rfT "${sicl}" src/lisp/kernel/contrib/sicl
+    cp -rfT "${cst}" src/lisp/kernel/contrib/Concrete-Syntax-Tree
+    cp -rfT "${c2mop}" src/lisp/kernel/contrib/closer-mop
+    cp -rfT "${acclimation}" src/lisp/kernel/contrib/Acclimation
+    cp -rfT "${eclector}" src/lisp/kernel/contrib/Eclector
+    cp -rfT "${alexandria}" src/lisp/kernel/contrib/alexandria
+    cp -rfT "${mps}" src/mps
+    cp -rfT "${asdf}" src/lisp/modules/asdf
+
+    chmod -R u+rwX src
+    ( cd src/lisp/modules/asdf; make )
   '';
 
   buildTargets = "build_cboehm";
   installTargets = "install_cboehm";
 
+  CLASP_SRC_DONTTOUCH = "true";
+
   meta = {
     inherit version;
     description = ''A Common Lisp implementation based on LLVM with C++ integration'';
     license = stdenv.lib.licenses.lgpl21Plus ;
     maintainers = [stdenv.lib.maintainers.raskin];
     platforms = stdenv.lib.platforms.linux;
+    # Large, long to build, a private build of clang is needed, a prerelease.
+    hydraPlatforms = [];
     homepage = "https://github.com/drmeister/clasp";
-    broken = true; # 2018-09-08, no successful build since 2018-01-03
   };
 }

pkgs/development/compilers/dmd/default.nix

@@ -1,11 +1,11 @@
 { stdenv, fetchFromGitHub
 , makeWrapper, unzip, which
-, curl, tzdata, gdb, darwin
+, curl, tzdata, gdb, darwin, git
 , callPackage, targetPackages, ldc
-, version ? "2.083.1"
+, version ? "2.084.0"
-, dmdSha256 ? "0b52yq7slgbrawb22kib9bk2x9xjiy6axwz1317fck5axl093d90"
+, dmdSha256 ? "1v61spdamncl8c1bzjc19b03p4jl0ih5zq9b7cqsy9ix7qaxmikf"
-, druntimeSha256 ? "1hm9p59ih21yv8x7cqjhkyy94677q4f8wk9fs9i1rybx8x19njyn"
+, druntimeSha256 ? "0vp414j6s11l9s54v81np49mv60ywmd7nnk41idkbwrq0nz4sfrq"
-, phobosSha256 ? "1zmz0f1wj0dgxy2cy63ljjc1sl2sgb7ij8bamlxw9nxrchwi3l43"
+, phobosSha256 ? "1wp7z1x299b0w9ny1ah2wrfhrs05vc4bk51csgw9774l3dqcnv53"
 }:
 
 let
@@ -42,50 +42,22 @@ let
 
     sourceRoot = ".";
 
+    # https://issues.dlang.org/show_bug.cgi?id=19553
+    hardeningDisable = [ "fortify" ];
+
     postUnpack = ''
         patchShebangs .
-
-        # Remove cppa test for now because it doesn't work.
-        rm dmd/test/runnable/cppa.d
-        rm dmd/test/runnable/extra-files/cppb.cpp
-    ''
-
-    + stdenv.lib.optionalString (stdenv.hostPlatform.isDarwin) ''
-        rm dmd/test/runnable/test16096.sh
-    '';
-
-    # Compile with PIC to prevent colliding modules with binutils 2.28.
-    # https://issues.dlang.org/show_bug.cgi?id=17375
-    usePIC = "-fPIC";
-
-    phobosPatches = ''
-        # Ugly hack so the dlopen call has a chance to succeed.
-        # https://issues.dlang.org/show_bug.cgi?id=15391
-        substituteInPlace phobos/std/net/curl.d \
-            --replace libcurl.so ${curl.out}/lib/libcurl.so
-
-        # phobos uses curl, so we need to patch the path to the lib.
-        substituteInPlace phobos/posix.mak \
-            --replace "-soname=libcurl.so.4" "-soname=${curl.out}/lib/libcurl.so.4"
-
     '';
 
     postPatch = ''
-        substituteInPlace druntime/test/common.mak \
+        substituteInPlace dmd/test/compilable/extra-files/ddocYear.html \
-            --replace "DFLAGS:=" "DFLAGS:=${usePIC} "
+            --replace "2018" "__YEAR__"
 
-        substituteInPlace dmd/src/posix.mak \
+        substituteInPlace dmd/test/runnable/test16096.sh \
-            --replace "DFLAGS :=" "DFLAGS += -link-defaultlib-shared=false"
+            --replace "{EXT}" "{EXE}"
-    ''
-
-    + phobosPatches
-
-    + stdenv.lib.optionalString stdenv.hostPlatform.isDarwin ''
-        substituteInPlace dmd/posix.mak \
-            --replace MACOSX_DEPLOYMENT_TARGET MACOSX_DEPLOYMENT_TARGET_
     '';
 
-    nativeBuildInputs = [ ldc makeWrapper unzip which gdb ]
+    nativeBuildInputs = [ ldc makeWrapper unzip which gdb git ]
 
     ++ stdenv.lib.optional stdenv.hostPlatform.isDarwin (with darwin.apple_sdk.frameworks; [
       Foundation
@@ -109,7 +81,8 @@ let
         make -j$NIX_BUILD_CORES -f posix.mak BUILD=release ENABLE_RELEASE=1 PIC=1 INSTALL_DIR=$out DMD=${pathToDmd}
         cd ../phobos
         echo ${tzdata}/share/zoneinfo/ > TZDatabaseDirFile
-        make -j$NIX_BUILD_CORES -f posix.mak BUILD=release ENABLE_RELEASE=1 PIC=1 INSTALL_DIR=$out DMD=${pathToDmd} DFLAGS="-version=TZDatabaseDir -J$(pwd)"
+        echo ${curl.out}/lib/libcurl.so > LibcurlPathFile
+        make -j$NIX_BUILD_CORES -f posix.mak BUILD=release ENABLE_RELEASE=1 PIC=1 INSTALL_DIR=$out DMD=${pathToDmd} DFLAGS="-version=TZDatabaseDir -version=LibcurlPath -J$(pwd)"
         cd ..
     '';
 
@@ -119,7 +92,7 @@ let
 
     checkPhase = ''
         cd dmd
-        make -j$NIX_BUILD_CORES -C test -f Makefile PIC=1 DMD=${pathToDmd} BUILD=release SHARED=0 SHELL=$SHELL
+        make -j$NIX_BUILD_CORES -C test -f Makefile PIC=1 CC=$CXX DMD=${pathToDmd} BUILD=release SHARED=0 SHELL=$SHELL
         cd ../druntime
         make -j$NIX_BUILD_CORES -f posix.mak unittest PIC=1 DMD=${pathToDmd} BUILD=release
         cd ..
@@ -194,15 +167,14 @@ let
 
       sourceRoot = ".";
 
-      postPatch = dmdBuild.phobosPatches;
-
       nativeBuildInputs = dmdBuild.nativeBuildInputs;
       buildInputs = dmdBuild.buildInputs;
 
       buildPhase = ''
           cd phobos
           echo ${tzdata}/share/zoneinfo/ > TZDatabaseDirFile
-          make -j$NIX_BUILD_CORES -f posix.mak unittest BUILD=release ENABLE_RELEASE=1 PIC=1 DMD=${dmdBuild}/bin/dmd DFLAGS="-version=TZDatabaseDir -J$(pwd)"
+          echo ${curl.out}/lib/libcurl.so > LibcurlPathFile
+          make -j$NIX_BUILD_CORES -f posix.mak unittest BUILD=release ENABLE_RELEASE=1 PIC=1 DMD=${dmdBuild}/bin/dmd DFLAGS="-version=TZDatabaseDir -version=LibcurlPath -J$(pwd)"
       '';
 
       installPhase = ''

pkgs/development/compilers/gcc-arm-embedded/8/default.nix

@@ -0,0 +1,39 @@
+{ stdenv, lib, fetchurl, ncurses5, python27 }:
+
+with lib;
+
+stdenv.mkDerivation rec {
+  name = "gcc-arm-embedded-${version}";
+  version = "8-2018-q4-major";
+  subdir = "8-2018q4";
+
+  urlString = "https://developer.arm.com/-/media/Files/downloads/gnu-rm/${subdir}/gcc-arm-none-eabi-${version}-linux.tar.bz2";
+
+  src = fetchurl { url=urlString; sha256="fb31fbdfe08406ece43eef5df623c0b2deb8b53e405e2c878300f7a1f303ee52"; };
+
+  phases = [ "unpackPhase" "installPhase" "fixupPhase" ];
+
+  installPhase = ''
+    mkdir -p $out
+    cp -r * $out
+  '';
+
+  dontPatchELF = true;
+  dontStrip = true;
+
+  preFixup = ''
+    find $out -type f | while read f; do
+      patchelf $f > /dev/null 2>&1 || continue
+      patchelf --set-interpreter $(cat ${stdenv.cc}/nix-support/dynamic-linker) "$f" || true
+      patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ "$out" stdenv.cc.cc ncurses5 python27 ]} "$f" || true
+    done
+  '';
+
+  meta = {
+    description = "Pre-built GNU toolchain from ARM Cortex-M & Cortex-R processors (Cortex-M0/M0+/M3/M4/M7, Cortex-R4/R5/R7/R8)";
+    homepage = https://developer.arm.com/open-source/gnu-toolchain/gnu-rm;
+    license = with licenses; [ bsd2 gpl2 gpl3 lgpl21 lgpl3 mit ];
+    maintainers = with maintainers; [ prusnak ];
+    platforms = platforms.linux;
+  };
+}

pkgs/development/coq-modules/category-theory/default.nix

@@ -33,7 +33,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ coq ] ++ (with coq.ocamlPackages; [ ocaml camlp5 findlib ]);
   propagatedBuildInputs = [ ssreflect equations ];
 
-  enableParallelBuilding = false;
+  buildFlags = [ "JOBS=$(NIX_BUILD_CORES)" ];
 
   installPhase = ''
     make -f Makefile.coq COQLIB=$out/lib/coq/${coq.coq-version}/ install

pkgs/development/interpreters/clojure/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "clojure-${version}";
-  version = "1.10.0.403";
+  version = "1.10.0.411";
 
   src = fetchurl {
     url = "https://download.clojure.org/install/clojure-tools-${version}.tar.gz";
-    sha256 = "0jsyd0vr1qfqs0dz560hyfya553jhr4m4msf5x0n610yzvbqym4c";
+    sha256 = "00bhn6w9iwhgmyx89lk97q19phpm9vh45m3m1pi7d31gldb6v0zh";
   };
 
   buildInputs = [ makeWrapper ];

pkgs/development/interpreters/php/default.nix

@@ -263,12 +263,10 @@ in {
   };
 
   php73 = generic {
-    version = "7.3.0";
+    version = "7.3.1";
-    sha256 = "0rvwx37dsmxivgrf4wfc1y778iln498c6a40biy9k6lnr6p7s9ks";
+    sha256 = "13iqfkz9rmx9vy106lvw1nbk88qgwdkvxam0l5s14r7jsw62pvxg";
 
-    # https://bugs.php.net/bug.php?id=71041
     # https://bugs.php.net/bug.php?id=76826
-    extraPatches = [ ./fix-bug-71041.patch ]
+    extraPatches = optional stdenv.isDarwin ./php73-darwin-isfinite.patch;
-      ++ optional stdenv.isDarwin ./php73-darwin-isfinite.patch;
   };
 }

pkgs/development/interpreters/tinyscheme/default.nix

@@ -0,0 +1,33 @@
+{ stdenv, fetchurl }:
+
+stdenv.mkDerivation rec {
+  name = "tinyscheme-${version}";
+  version = "1.41";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/tinyscheme/${name}.tar.gz";
+    sha256 = "168rk4zrlhsknbvldq2jsgabpwlqkx6la44gkqmijmf7jhs11h7a";
+  };
+
+  patchPhase = ''
+    substituteInPlace scheme.c --replace "init.scm" "$out/lib/init.scm"
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin $out/lib
+    cp init.scm $out/lib
+    cp scheme $out/bin/tinyscheme
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Lightweight Scheme implementation";
+    longDescription = ''
+      TinyScheme is a lightweight Scheme interpreter that implements as large a
+      subset of R5RS as was possible without getting very large and complicated.
+    '';
+    homepage = http://tinyscheme.sourceforge.net/;
+    license = licenses.bsdOriginal;
+    maintainers = [ maintainers.ebzzry ];
+    platforms = platforms.unix;
+  };
+}

pkgs/development/libraries/boehm-gc/default.nix

@@ -25,7 +25,8 @@ stdenv.mkDerivation rec {
   '';
 
   patches = [ (fetchpatch {
-    url = "https://gitweb.gentoo.org/proj/musl.git/plain/dev-libs/boehm-gc/files/boehm-gc-7.6.0-sys_select.patch";
+    name = "boehm-gc-7.6.0-sys_select.patch";
+    url = "https://gitweb.gentoo.org/proj/musl.git/plain/dev-libs/boehm-gc/files/boehm-gc-7.6.0-sys_select.patch?id=85b6a600996bdd71162b357e9ba93d8559342432";
     sha256 = "1gydwlklvci30f5dpp5ccw2p2qpph5y41r55wx9idamjlq66fbb3";
   }) ] ++
     # https://github.com/ivmai/bdwgc/pull/208

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

@@ -96,7 +96,7 @@
 , libxcbshapeExtlib ? true # X11 grabbing shape rendering
 , libXv ? null # Xlib support
 , lzma ? null # xz-utils
-, nvenc ? false, nvidia-video-sdk ? null # NVIDIA NVENC support
+, nvenc ? false, nvidia-video-sdk ? null, nv-codec-headers ? null # NVIDIA NVENC support
 , callPackage # needed for NVENC to access external ffmpeg nvidia headers
 , openal ? null # OpenAL 1.1 capture support
 #, opencl ? null # OpenCL code
@@ -176,8 +176,6 @@
 let
   inherit (stdenv) isCygwin isFreeBSD isLinux;
   inherit (stdenv.lib) optional optionals optionalString enableFeature;
-
-  nv-codec-headers = callPackage ./nv-codec-headers.nix { };
 in
 
 /*

pkgs/development/libraries/git2/0.27.nix

@@ -0,0 +1,36 @@
+{ stdenv, fetchFromGitHub, cmake, pkgconfig, python
+, zlib, libssh2, openssl, http-parser, curl
+, libiconv, Security
+}:
+
+stdenv.mkDerivation rec {
+  version = "0.27.7";
+  name = "libgit2-${version}";
+
+  src = fetchFromGitHub {
+    owner = "libgit2";
+    repo = "libgit2";
+    rev = "v${version}";
+    sha256 = "1q3mp7xjpbmdsnk4sdzf2askbb4pgbxcmr1h7y7zk2738dndwkha";
+  };
+
+  cmakeFlags = [ "-DTHREADSAFE=ON" ];
+
+  nativeBuildInputs = [ cmake python pkgconfig ];
+
+  buildInputs = [ zlib libssh2 openssl http-parser curl ]
+    ++ stdenv.lib.optional stdenv.isDarwin Security;
+
+  propagatedBuildInputs = stdenv.lib.optional (!stdenv.isLinux) libiconv;
+
+  enableParallelBuilding = true;
+
+  doCheck = false; # hangs. or very expensive?
+
+  meta = {
+    description = "The Git linkable library";
+    homepage = https://libgit2.github.com/;
+    license = stdenv.lib.licenses.gpl2;
+    platforms = with stdenv.lib.platforms; all;
+  };
+}

pkgs/development/libraries/git2/default.nix

@@ -1,18 +1,18 @@
-{ stdenv, fetchFromGitHub, cmake, pkgconfig, python
+{ stdenv, fetchFromGitHub, pkgconfig, cmake
-, zlib, libssh2, openssl, http-parser, curl
+, zlib, python, libssh2, openssl, curl, http-parser
 , libiconv, Security
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (rec {
-  pname = "libgit2";
+  name = "libgit2-${version}";
-  version = "0.27.7";
+  version = "0.26.6";
   # keep the version in sync with pythonPackages.pygit2 and libgit2-glib
 
   src = fetchFromGitHub {
     owner = "libgit2";
     repo = "libgit2";
     rev = "v${version}";
-    sha256 = "1q3mp7xjpbmdsnk4sdzf2askbb4pgbxcmr1h7y7zk2738dndwkha";
+    sha256 = "17pjvprmdrx4h6bb1hhc98w9qi6ki7yl57f090n9kbhswxqfs7s3";
   };
 
   cmakeFlags = [ "-DTHREADSAFE=ON" ];
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ zlib libssh2 openssl http-parser curl ]
     ++ stdenv.lib.optional stdenv.isDarwin Security;
 
-  propagatedBuildInputs = stdenv.lib.optional (!stdenv.isLinux) libiconv;
+  propagatedBuildInputs = stdenv.lib.optional (!stdenv.isLinux) [ libiconv ];
 
   enableParallelBuilding = true;
 
@@ -34,4 +34,5 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2;
     platforms = with platforms; all;
   };
-}
+} // stdenv.lib.optionalAttrs (!stdenv.isLinux) {
+})

pkgs/development/libraries/gstreamer/ges/default.nix

@@ -32,4 +32,8 @@ stdenv.mkDerivation rec {
     })
     ./fix_pkgconfig_includedir.patch
   ];
+
+  postPatch = ''
+    sed -i -r -e 's/p(bad|good) = .*/p\1 = pbase/' tests/check/meson.build
+  '';
 }

pkgs/development/libraries/libbladeRF/default.nix

@@ -1,15 +1,25 @@
 { stdenv, lib, fetchFromGitHub, fetchpatch, pkgconfig, cmake, git, doxygen, help2man, ncurses, tecla
 , libusb1, udev }:
 
-stdenv.mkDerivation rec {
+let
-  version = "2.0.2";
+  # fetch submodule
+  noos = fetchFromGitHub {
+    owner = "analogdevicesinc";
+    repo = "no-OS";
+    rev = "0bba46e6f6f75785a65d425ece37d0a04daf6157";
+    sha256 = "0is79dhsyp9xmlnfdr1i5s1c22ipjafk9d35jpn5dynpvj86m99c";
+  };
+
+  version = "2.2.0";
+
+in stdenv.mkDerivation {
   name = "libbladeRF-${version}";
 
   src = fetchFromGitHub {
     owner = "Nuand";
     repo = "bladeRF";
     rev = "libbladeRF_v${version}";
-    sha256 = "18qwljjdnf4lds04kc1zvslr5hh9cjnnjkcy07lbkrq7pj0pfnc6";
+    sha256 = "0mdj5dkqg69gp0xw6gkhp86nxnm9g7az5rplnncxkp4p1kr35rnl";
   };
 
   nativeBuildInputs = [ pkgconfig ];
@@ -18,18 +28,14 @@ stdenv.mkDerivation rec {
     ++ lib.optionals stdenv.isLinux [ udev ]
     ++ lib.optionals stdenv.isDarwin [ ncurses ];
 
+
+  postUnpack = ''
+    cp -r ${noos}/* source/thirdparty/analogdevicesinc/no-OS/
+  '';
+
   # Fixup shebang
   prePatch = "patchShebangs host/utilities/bladeRF-cli/src/cmd/doc/generate.bash";
 
-  # Fixes macos and freebsd compilation issue.
-  # https://github.com/Nuand/bladeRF/commit/0cb4ea888543b2dc75b876f7024e180854fbe9c3
-  patches = [ (fetchpatch {
-                name = "fix-OSX-and-FreeBSD-build.patch";
-                url = "https://github.com/Nuand/bladeRF/commit/0cb4ea88.diff";
-                sha256 = "1ccpa69vz2nlpdnxprh4rd1pgphk82z5lfmbrfdkn7srw6nxl469";
-              })
-            ];
-
   # Let us avoid nettools as a dependency.
   postPatch = ''
     sed -i 's/$(hostname)/hostname/' host/utilities/bladeRF-cli/src/cmd/doc/generate.bash

pkgs/development/libraries/libmediaart/default.nix

@@ -14,7 +14,9 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ meson ninja pkgconfig vala gtk-doc docbook_xsl docbook_xml_dtd_412 gobject-introspection ];
   buildInputs = [ glib gdk_pixbuf ];
 
-  doCheck = true;
+  # FIXME: Turn on again when https://github.com/NixOS/nixpkgs/issues/53701
+  # is fixed on master.
+  doCheck = false;
 
   passthru = {
     updateScript = gnome3.updateScript {

pkgs/development/libraries/libngspice/default.nix

@@ -2,12 +2,13 @@
 
 # Note that this does not provide the ngspice command-line utility. For that see
 # the ngspice derivation.
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
-  name = "libngspice-29";
+  name = "libngspice-${version}";
+  version = "30";
 
   src = fetchurl {
-    url = "mirror://sourceforge/ngspice/ngspice-29.tar.gz";
+    url = "mirror://sourceforge/ngspice/ngspice-${version}.tar.gz";
-    sha256 = "0jjwz73naq7l9yhwdqbpnrfckywp2ffkppivxjv8w92zq7xhyvcd";
+    sha256 = "15v0jdfy2a2zxp8dmy04fdp7w7a4vwvffcwa688r81b86wphxzh8";
   };
 
   nativeBuildInputs = [ flex bison ];

pkgs/development/libraries/mps/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mps-${version}";
-  version = "1.116.0";
+  version = "1.117.0";
 
   src = fetchurl {
     url    = "https://www.ravenbrook.com/project/mps/release/${version}/mps-kit-${version}.tar.gz";
-    sha256 = "1k7vnanpgawnj84x2xs6md57pfib9p7c3acngqzkl3c2aqw8qay0";
+    sha256 = "04ix4l7lk6nxxk9sawpnxbybvqb82lks5606ym10bc1qbc2kqdcz";
   };
 
   nativeBuildInputs = [ autoreconfHook ];
@@ -15,6 +15,7 @@ stdenv.mkDerivation rec {
   # needed for 1.116.0 to build with gcc7
   NIX_CFLAGS_COMPILE = [
     "-Wno-implicit-fallthrough"
+    "-Wno-error=clobbered"
   ];
 
 

pkgs/development/libraries/nv-codec-headers/default.nix

@@ -2,18 +2,18 @@
 
 stdenv.mkDerivation rec {
   name = "nv-codec-headers-${version}";
-  version = "n8.1.24.2";
+  version = "8.2.15.6";
 
   src = fetchgit {
     url = "https://git.videolan.org/git/ffmpeg/nv-codec-headers.git";
-    rev = "${version}";
+    rev = "n${version}";
-    sha256 = "122i3f6whiz5yp44dhk73ifr1973z8vvfbg4216vb782bl8b5bam";
+    sha256 = "0216ww8byjxz639kagyw0mr9vxxwj89xdnj448d579vjr54jychv";
   };
 
   makeFlags = [ "PREFIX=$(out)" ];
 
   meta = {
-    description = "ffmpeg nvidia headers for NVENC";
+    description = "FFmpeg version of headers for NVENC";
     homepage = http://ffmpeg.org/;
     license = stdenv.lib.licenses.gpl3Plus;
     maintainers = [ stdenv.lib.maintainers.MP2E ];

pkgs/development/libraries/openwsman/default.nix

@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   name = "openwsman-${version}";
-  version = "2.6.5";
+  version = "2.6.9";
 
   src = fetchFromGitHub {
     owner  = "Openwsman";
     repo   = "openwsman";
     rev    = "v${version}";
-    sha256 = "1r0zslgpcr4m20car4s3hsccy10xcb39qhpw3dhpjv42xsvvs5xv";
+    sha256 = "19s5h551ppxmi2kljf8z58jjc6yrpczbxdrl4hh2l4jxv7iphk5i";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
@@ -18,6 +18,8 @@ stdenv.mkDerivation rec {
 
   cmakeFlags = [
     "-DCMAKE_BUILD_RUBY_GEM=no"
+    "-DBUILD_PYTHON=no"
+    "-DBUILD_PYTHON3=yes"
   ];
 
   preConfigure = ''

pkgs/development/libraries/physics/hoppet/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, gfortran }:
+{ stdenv, fetchurl, gfortran, perl }:
 
 stdenv.mkDerivation rec {
   name = "hoppet-${version}";
@@ -10,9 +10,14 @@ stdenv.mkDerivation rec {
   };
 
   buildInputs = [ gfortran ];
+  nativeBuildInputs = [ perl ];
 
   enableParallelBuilding = true;
 
+  preConfigure = ''
+    patchShebangs .
+  '';
+
   meta = with stdenv.lib; {
     description = "Higher Order Perturbative Parton Evolution Toolkit";
     license     = licenses.gpl2;

pkgs/development/libraries/termbox/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, python3, wafHook }:
+{ stdenv, fetchFromGitHub, python3, wafHook, fetchpatch }:
 
 stdenv.mkDerivation rec {
   name = "termbox-${version}";
@@ -9,7 +9,18 @@ stdenv.mkDerivation rec {
     rev = "v${version}";
     sha256 = "08yqxzb8fny8806p7x8a6f3phhlbfqdd7dhkv25calswj7w1ssvs";
   };
+
+  # patch which updates the `waf` version used to build
+  # to make the package buildable on Python 3.7
+  patches = [
+    (fetchpatch {
+      url = https://github.com/nsf/termbox/commit/6fe63ac3ad63dc2c3ac45b770541cc8b7a1d2db7.patch;
+      sha256 = "1s5747v51sdwvpsg6k9y1j60yn9f63qnylkgy8zrsifjzzd5fzl6";
+    })
+  ];
+
   nativeBuildInputs = [ python3 wafHook ];
+
   meta = with stdenv.lib; {
     description = "Library for writing text-based user interfaces";
     license = licenses.mit;

pkgs/development/ocaml-modules/resource-pooling/default.nix

@@ -0,0 +1,35 @@
+{ stdenv, fetchFromGitHub, ocaml, findlib, ocamlbuild, lwt_log }:
+
+let pname = "resource-pooling"; in
+
+if !stdenv.lib.versionAtLeast ocaml.version "4.06"
+then throw "${pname} is not available for OCaml ${ocaml.version}"
+else
+
+stdenv.mkDerivation rec {
+  version = "0.5.2";
+  name = "ocaml${ocaml.version}-${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "ocsigen";
+    repo = pname;
+    rev = version;
+    sha256 = "00rz1i61w2dy108hzv38rblnsv6b56b5a1mk5h3zddpivcljp2dh";
+  };
+
+  buildInputs = [ ocaml findlib ocamlbuild ];
+  propagatedBuildInputs = [ lwt_log ];
+
+  configurePhase = "ocaml setup.ml -configure --prefix $out";
+  buildPhase = "ocaml setup.ml -build";
+  createFindlibDestdir = true;
+  installPhase = "ocaml setup.ml -install";
+
+  meta = {
+    inherit (src.meta) homepage;
+    inherit (ocaml.meta) platforms;
+    description = "A library for pooling resources like connections, threads, or similar";
+    license = stdenv.lib.licenses.mit;
+    maintainers = [ stdenv.lib.maintainers.vbgl ];
+  };
+}

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

@@ -8,33 +8,37 @@
 , async-timeout
 , yarl
 , idna-ssl
+, typing-extensions
+, pytestrunner
 , pytest
 , gunicorn
-, pytest-mock
-, async_generator
-, pytestrunner
 , pytest-timeout
+, async_generator
+, pytest_xdist
+, pytestcov
+, pytest-mock
+, trustme
+, brotlipy
 }:
 
 buildPythonPackage rec {
   pname = "aiohttp";
-  version = "3.4.4";
+  version = "3.5.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1ykm6kdjkrg556j0zd7dx2l1rsrbh0d9g27ivr6dmaahz9pyrbsi";
+    sha256 = "7967b760d0e96eb7ac6b20a9143112ce5c03a00b4f74d8a5ee66c8e88e6b6800";
   };
 
   disabled = pythonOlder "3.5";
 
-  checkInputs = [ pytest gunicorn pytest-mock async_generator pytestrunner pytest-timeout ];
+  checkInputs = [
+    pytestrunner pytest gunicorn pytest-timeout async_generator pytest_xdist
+    pytest-mock pytestcov trustme brotlipy
+  ];
 
   propagatedBuildInputs = [ attrs chardet multidict async-timeout yarl ]
-    ++ lib.optional (pythonOlder "3.7") idna-ssl;
+    ++ lib.optionals (pythonOlder "3.7") [ idna-ssl typing-extensions ];
-
-
-  # Several test failures. Need to be looked into.
-  doCheck = false;
 
   meta = with lib; {
     description = "Asynchronous HTTP Client/Server for Python and asyncio";

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

@@ -0,0 +1,33 @@
+{ lib, buildPythonPackage, fetchPypi
+, redis
+, memcached
+, msgpack-python
+}:
+
+buildPythonPackage rec {
+  pname = "cachy";
+  version = "0.2.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0v6mjyhgx6j7ya20bk69cr3gdzdkdf6psay0h090rscclgji65dp";
+  };
+
+  propagatedBuildInputs = [
+    redis
+    memcached
+    msgpack-python
+  ];
+
+  # The Pypi tarball doesn't include tests, and the GitHub source isn't
+  # buildable until we bootstrap poetry, see
+  # https://github.com/NixOS/nixpkgs/pull/53599#discussion_r245855665
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/cachy;
+    description = "Cachy provides a simple yet effective caching library";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

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

@@ -0,0 +1,30 @@
+{ lib, buildPythonPackage, fetchPypi
+, pylev, pastel, clikit }:
+
+buildPythonPackage rec {
+  pname = "cleo";
+  version = "0.7.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "091nzpfp5incd2fzqych78rvyx4i3djr50cnizbjzr3dc7g00l3s";
+  };
+
+  propagatedBuildInputs = [
+    pylev
+    pastel
+    clikit
+  ];
+
+  # The Pypi tarball doesn't include tests, and the GitHub source isn't
+  # buildable until we bootstrap poetry, see
+  # https://github.com/NixOS/nixpkgs/pull/53599#discussion_r245855665
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/cleo;
+    description = "Allows you to create beautiful and testable command-line interfaces";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

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

@@ -0,0 +1,30 @@
+{ lib, buildPythonPackage, fetchPypi
+, isPy27, isPy34
+, pylev, pastel, typing, enum34 }:
+
+buildPythonPackage rec {
+  pname = "clikit";
+  version = "0.2.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0zr1s0xhk62p9a6zcp5whvsb27lddyk8gx03k9l8q18jp7y3igbv";
+  };
+
+  propagatedBuildInputs = [
+    pylev pastel
+  ] ++ lib.optional (isPy27 || isPy34) typing
+    ++ lib.optional isPy27 enum34;
+
+  # The Pypi tarball doesn't include tests, and the GitHub source isn't
+  # buildable until we bootstrap poetry, see
+  # https://github.com/NixOS/nixpkgs/pull/53599#discussion_r245855665
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/clikit;
+    description = "A group of utilities to build beautiful and testable command line interfaces";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

pkgs/development/python-modules/fido2/default.nix

@@ -1,4 +1,7 @@
-{ lib, buildPythonPackage, fetchPypi, six, cryptography }:
+{ lib, buildPythonPackage, fetchPypi
+, six, cryptography
+, mock, pyfakefs
+}:
 
 buildPythonPackage rec {
   pname = "fido2";
@@ -9,12 +12,10 @@ buildPythonPackage rec {
     sha256 = "1pl8d2pr6jzqj4y9qiaddhjgnl92kikjxy0bgzm2jshkzzic8mp3";
   };
 
-  # The pypi package does not include tests
-  # Check https://github.com/Yubico/python-fido2/pull/8
-  doCheck = false;
-
   propagatedBuildInputs = [ six cryptography ];
 
+  checkInputs = [ mock pyfakefs ];
+
   meta = with lib; {
     description = "Provides library functionality for FIDO 2.0, including communication with a device over USB.";
     homepage = https://github.com/Yubico/python-fido2;

pkgs/development/python-modules/google-i18n-address/default.nix

@@ -0,0 +1,22 @@
+{ buildPythonPackage, fetchPypi, lib, requests, pytest, pytestcov, mock }:
+
+buildPythonPackage rec {
+  pname = "google-i18n-address";
+  version = "2.3.4";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0f1j1lp9bmllkzhciw0lxi7ipm8w461n0p97mz9714br0cs9glm1";
+  };
+
+  propagatedBuildInputs = [ requests ];
+
+  checkInputs = [ pytest pytestcov mock ];
+
+  meta = with lib; {
+    description = "Google's i18n address data packaged for Python";
+    homepage = https://pypi.org/project/google-i18n-address/;
+    maintainers = with maintainers; [ ma27 ];
+    license = licenses.bsd3;
+  };
+}

pkgs/development/python-modules/h5py/default.nix

@@ -10,12 +10,12 @@ let
   mpi = hdf5.mpi;
   mpiSupport = hdf5.mpiSupport;
 in buildPythonPackage rec {
-  version = "2.8.0";
+  version = "2.9.0";
   pname = "h5py";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0mdr6wrq02ac93m1aqx9kad0ppfzmm4imlxqgyy1x4l7hmdcc9p6";
+    sha256 = "9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002";
   };
 
   configure_flags = "--hdf5=${hdf5}" + optionalString mpiSupport " --mpi";
@@ -37,9 +37,6 @@ in buildPythonPackage rec {
   propagatedBuildInputs = [ numpy six]
     ++ optionals mpiSupport [ mpi4py openssh ];
 
-  # https://github.com/h5py/h5py/issues/1088
-  doCheck = false;
-
   meta = {
     description =
       "Pythonic interface to the HDF5 binary data format";

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

@@ -1,6 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, glibcLocales
 }:
 
 buildPythonPackage rec {
@@ -12,6 +13,10 @@ buildPythonPackage rec {
     sha256 = "8eec9c1f4bfae3408a3f30500261f7e6a65912dc138526ea054f9ad98892e9d2";
   };
 
+  buildInputs = [ glibcLocales ];
+
+  LANG = "en_US.UTF-8";
+
   meta = with stdenv.lib; {
     description = "Pure-Python HPACK header compression";
     homepage = "http://hyper.rtfd.org";

pkgs/development/python-modules/mt-940/default.nix

@@ -3,14 +3,15 @@
 }:
 
 buildPythonPackage rec {
-  version = "4.12.2";
+  version = "4.13.0";
   pname = "mt-940";
 
+  # No tests in PyPI tarball
   src = fetchFromGitHub {
     owner = "WoLpH";
     repo = "mt940";
     rev = "v${version}";
-    sha256 = "0l7q8v00dhpbc9mh6baaaqc55kf44rszygx28dq3pwp5b5x33nir";
+    sha256 = "0p6z4ipj0drph3ryn8mnb3xn0vjfv54y1c5w5i9ixrxwz48h6bga";
   };
 
   postPatch = ''
@@ -24,9 +25,8 @@ buildPythonPackage rec {
 
   checkInputs = [ pyyaml pytestpep8 pytestflakes pytest glibcLocales ];
 
-  # See https://github.com/WoLpH/mt940/issues/64 for the disabled test
   checkPhase = ''
-    py.test -k "not mt940.models.FixedOffset"
+    py.test
   '';
 
   meta = with stdenv.lib; {

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

@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "multidict";
-  version = "4.4.2";
+  version = "4.5.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3c11e92c3dfc321014e22fb442bc9eb70e01af30d6ce442026b0c35723448c66";
+    sha256 = "024b8129695a952ebd93373e45b5d341dbb87c17ce49637b34000093f243dd4f";
   };
 
   checkInputs = [ pytest pytestrunner pytestcov ];

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "netdisco";
-  version = "2.2.0";
+  version = "2.3.0";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b5e810721a266660f7f90fc43f12c4635ec95c3db87d9e30ca408bb922cb1007";
+    sha256 = "2571fc094f3bf8c60be211e90474515f565f3ef1c92e857176daab8577493a3b";
   };
 
   propagatedBuildInputs = [ requests zeroconf netifaces ];

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

@@ -30,21 +30,28 @@
 , which
 , bash
 , glibcLocales
+, callPackage
 }:
 
 assert !isPy3k -> configparser != null;
 
+let
+
+ # This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo.
+ neurdflib = callPackage ./neurdflib.nix { };
+
+in
+
 buildPythonPackage rec {
   pname = "nipype";
-  version = "1.1.5";
+  version = "1.1.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "d49bbe531cdbf0a049f1581e4d3c63231ff5978445cb380aa6e7f8f1d256a29c";
+    sha256 = "0iyi5w2h42bpssqj52ixm2kxp56yxfxdacb6xv5r24yv3hmwd4yn";
   };
 
-  # see https://github.com/nipy/nipype/issues/2240
+  patches = [ ./move-uneeded-requires.patch ];
-  patches = [ ./prov-version.patch ];
 
   postPatch = ''
     substituteInPlace nipype/interfaces/base/tests/test_core.py \
@@ -57,6 +64,7 @@ buildPythonPackage rec {
     funcsigs
     future
     networkx
+    neurdflib
     nibabel
     numpy
     packaging
@@ -72,12 +80,24 @@ buildPythonPackage rec {
     futures
   ];
 
-  checkInputs = [ pytest mock pytestcov pytest_xdist pytest-forked codecov which glibcLocales ];
+  checkInputs = [
+    codecov
+    glibcLocales
+    mock
+    pytest
+    pytest-forked
+    pytest_xdist
+    pytestcov
+    which
+  ];
 
   checkPhase = ''
-    LC_ALL="en_US.UTF-8" py.test -v --doctest-modules nipype
+    LC_ALL="en_US.UTF-8" pytest -v --doctest-modules nipype
   '';
 
+  # See: https://github.com/nipy/nipype/issues/2839
+  doCheck = false;
+
   meta = with stdenv.lib; {
     homepage = http://nipy.org/nipype/;
     description = "Neuroimaging in Python: Pipelines and Interfaces";

pkgs/development/python-modules/nipype/move-uneeded-requires.patch

@@ -0,0 +1,31 @@
+diff --git a/nipype/info.py b/nipype/info.py
+index c6503ac..4379643 100644
+--- a/nipype/info.py
++++ b/nipype/info.py
+@@ -147,9 +147,6 @@ REQUIRES = [
+     'neurdflib',
+     'click>=%s' % CLICK_MIN_VERSION,
+     'funcsigs',
+-    'pytest>=%s' % PYTEST_MIN_VERSION,
+-    'pytest-xdist',
+-    'mock',
+     'pydotplus',
+     'pydot>=%s' % PYDOT_MIN_VERSION,
+     'packaging',
+@@ -159,7 +156,15 @@ REQUIRES = [
+ if sys.version_info <= (3, 4):
+     REQUIRES.append('configparser')
+ 
+-TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env', 'coverage<5']
++TESTS_REQUIRES = [
++    'pytest>=%s' % PYTEST_MIN_VERSION,
++    'pytest-xdist',
++    'mock',
++    'pytest-cov',
++    'codecov',
++    'pytest-env',
++    'coverage<5'
++]
+ 
+ EXTRA_REQUIRES = {
+     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],

pkgs/development/python-modules/nipype/neurdflib.nix

@@ -0,0 +1,38 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, isodate
+, html5lib
+, SPARQLWrapper
+, networkx
+, nose
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "neurdflib";
+  version = "5.0.0.post1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1qgmprixqxycxpjk9wjdmjykma14qqa2wcbx4nsldxi0ga7i7vv5";
+  };
+
+  propagatedBuildInputs = [ isodate html5lib SPARQLWrapper ];
+
+  checkInputs = [ networkx nose ];
+
+  # Python 2 syntax
+  # Failing doctest
+  doCheck = false;
+
+  checkPhase = ''
+    ${python.interpreter} run_tests.py
+  '';
+
+  meta = with lib; {
+    description = "A temporary convenience package for changes waiting to be merged into the primary rdflib repo";
+    homepage = https://pypi.org/project/neurdflib;
+    license = licenses.bsd3;
+  };
+}

pkgs/development/python-modules/nipype/prov-version.patch

@@ -1,21 +0,0 @@
-diff --git a/nipype/info.py b/nipype/info.py
-index 1daa382e2..da338d0ea 100644
---- a/nipype/info.py
-+++ b/nipype/info.py
-@@ -108,7 +108,6 @@ DATEUTIL_MIN_VERSION = '2.2'
- PYTEST_MIN_VERSION = '3.0'
- FUTURE_MIN_VERSION = '0.16.0'
- SIMPLEJSON_MIN_VERSION = '3.8.0'
--PROV_VERSION = '1.5.0'
- CLICK_MIN_VERSION = '6.6.0'
- PYDOT_MIN_VERSION = '1.2.3'
- 
-@@ -140,7 +139,7 @@ REQUIRES = [
-     'traits>=%s' % TRAITS_MIN_VERSION,
-     'future>=%s' % FUTURE_MIN_VERSION,
-     'simplejson>=%s' % SIMPLEJSON_MIN_VERSION,
--    'prov==%s' % PROV_VERSION,
-+    'prov<2',
-     'click>=%s' % CLICK_MIN_VERSION,
-     'funcsigs',
-     'pytest>=%s' % PYTEST_MIN_VERSION,

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

@@ -0,0 +1,26 @@
+{ lib, buildPythonPackage, fetchFromGitHub, isPy3k, pytest }:
+
+buildPythonPackage rec {
+  pname = "pastel";
+  version = "0.1.0";
+
+  # No tests in PyPi tarball
+  src = fetchFromGitHub {
+    owner = "sdispater";
+    repo = "pastel";
+    rev = version;
+    sha256 = "1b4ag7jr7j0sxly5g29imdq8g0d4ixhbck55dblr45mlsidydx0s";
+  };
+
+  checkInputs = [ pytest ];
+  checkPhase = ''
+    pytest tests -sq
+  '';
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/pastel;
+    description = "Bring colors to your terminal";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

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

@@ -0,0 +1,35 @@
+{ stdenv
+, python
+, fetchPypi
+, buildPythonPackage
+, postgresql }:
+
+buildPythonPackage rec {
+  pname = "pgsanity";
+  version = "0.2.9";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "de0bbd6fe4f98bf5139cb5f466eac2e2abaf5a7b050b9e4867b87bf360873173";
+  };
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover -s test
+  '';
+
+  propagatedBuildInputs = [ postgresql ];
+
+  meta = with stdenv.lib; {
+    homepage = "http://github.com/markdrago/pgsanity";
+    description = "Checks the syntax of Postgresql SQL files";
+    longDescription = ''
+      PgSanity checks the syntax of Postgresql SQL files by
+      taking a file that has a list of bare SQL in it, 
+      making that file look like a C file with embedded SQL, 
+      run it through ecpg and 
+      let ecpg report on the syntax errors of the SQL.
+    '';
+    license = stdenv.lib.licenses.mit;
+    maintainers = with maintainers; [ nalbyuites ];
+  };
+}

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

@@ -1,21 +1,21 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, nose
 , pygments
-, isPy3k
 }:
 
 buildPythonPackage rec {
-  version = "0.8.0";
+  version = "0.9.2";
   pname = "piep";
-  disabled = isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1wgkg1kc28jpya5k4zvbc9jmpa60b3d5c3gwxfbp15hw6smyqirj";
+    sha256 = "0b5anpsq16xkiisws95jif5s5mplkl1kdnhy0w0i6m0zcy50jnxq";
   };
 
   propagatedBuildInputs = [ pygments ];
+  checkInputs = [ nose ];
 
   meta = with stdenv.lib; {
     description = "Bringing the power of python to stream editing";

pkgs/development/python-modules/pika-pool/default.nix

@@ -11,6 +11,10 @@ buildPythonPackage rec {
     sha256 = "f3985888cc2788cdbd293a68a8b5702a9c955db6f7b8b551aeac91e7f32da397";
   };
 
+  postPatch = ''
+    substituteInPlace setup.py --replace "pika >=0.9,<0.11" "pika"
+  '';
+
   # Tests require database connections
   doCheck = false;
 

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

@@ -0,0 +1,76 @@
+{ lib, buildPythonPackage, fetchPypi, callPackage
+, isPy27, isPy34
+, cleo
+, requests
+, cachy
+, requests-toolbelt
+, pyrsistent
+, pyparsing
+, cachecontrol
+, pkginfo
+, html5lib
+, shellingham
+, tomlkit
+, typing
+, pathlib2
+, virtualenv
+, functools32
+, pytest
+}:
+
+let
+  cleo6 = cleo.overrideAttrs (oldAttrs: rec {
+    version = "0.6.8";
+    src = fetchPypi {
+      inherit (oldAttrs) pname;
+      inherit version;
+      sha256 = "06zp695hq835rkaq6irr1ds1dp2qfzyf32v60vxpd8rcnxv319l5";
+    };
+  });
+
+  jsonschema3 = callPackage ./jsonschema.nix { };
+
+in buildPythonPackage rec {
+  pname = "poetry";
+  version = "0.12.10";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "00npb0jlimnk4r01zkhfmns4843j1hfhd388s326da5pd8n0dq7l";
+  };
+
+  postPatch = ''
+    substituteInPlace pyproject.toml --replace "3.0a3" "3.0.0a3"
+    substituteInPlace setup.py --replace "3.0a3" "3.0.0a3"
+  '';
+
+  propagatedBuildInputs = [
+    cleo6
+    requests
+    cachy
+    requests-toolbelt
+    jsonschema3
+    pyrsistent
+    pyparsing
+    cachecontrol
+    pkginfo
+    html5lib
+    shellingham
+    tomlkit
+  ] ++ lib.optionals (isPy27 || isPy34) [ typing pathlib2 ]
+    ++ lib.optionals isPy27 [ virtualenv functools32 ];
+
+  # No tests in Pypi tarball
+  doCheck = false;
+  checkInputs = [ pytest ];
+  checkPhase = ''
+    pytest tests
+  '';
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/poetry;
+    description = "Python dependency management and packaging made easy";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

pkgs/development/python-modules/poetry/jsonschema.nix

@@ -0,0 +1,37 @@
+{ lib, buildPythonPackage, fetchPypi, isPy27, callPackage
+, attrs
+, pyrsistent
+, six
+, functools32
+, lockfile
+, setuptools_scm
+}:
+
+buildPythonPackage rec {
+  pname = "jsonschema";
+  version = "3.0.0a3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "0pkhsq91rhk6384p0jxjkhc9yml2ya2l0mysyq78sb4981h45n6z";
+  };
+
+  nativeBuildInputs = [ setuptools_scm ];
+  propagatedBuildInputs = [
+    attrs
+    pyrsistent
+    six
+    lockfile
+  ] ++ lib.optional isPy27 functools32;
+
+  # tests for latest version rely on custom version of betterpaths that is
+  # difficult to deal with and isn't used on master
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/Julian/jsonschema;
+    description = "An implementation of JSON Schema validation for Python";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

pkgs/development/python-modules/py3status/default.nix

@@ -19,11 +19,11 @@
 
 buildPythonPackage rec {
   pname = "py3status";
-  version = "3.14";
+  version = "3.15";
   
   src = fetchPypi {
     inherit pname version;
-    sha256 = "8775fb3903458a519593fc22b712ccac598464e319a12b9fdf04803fa60a1583";
+    sha256 = "78aa7fa0af707641e215ea93bfd4bb5fd47f18a7193d84ed60bb9e6cccb75b7f";
   };
 
   doCheck = false;

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

@@ -1,5 +1,18 @@
 { stdenv, buildPythonPackage, fetchPypi, thrift, isPy3k }:
 
+let
+
+  thrift' = thrift.overridePythonAttrs (old: rec {
+    version = "0.9.3";
+    src= fetchPypi {
+      inherit (old) pname;
+      inherit version;
+      sha256 = "0zl7cgckqy9j5vq8wyfzw82q1blkdpsblnmhv8c6ffcxs4xkvg6z";
+    };
+  });
+
+in
+
 buildPythonPackage rec {
   pname = "pycassa";
   version = "1.11.2";
@@ -15,7 +28,7 @@ buildPythonPackage rec {
   # running
   doCheck = false;
 
-  propagatedBuildInputs = [ thrift ];
+  propagatedBuildInputs = [ thrift' ];
 
   meta = {
     description = "A python client library for Apache Cassandra";

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

@@ -1,7 +1,7 @@
 { stdenv, buildPythonPackage, fetchFromGitHub, python, pytest, glibcLocales }:
 
 buildPythonPackage rec {
-  version = "3.4.3";
+  version = "3.5.5";
   pname = "pyfakefs";
 
   # no tests in PyPI tarball
@@ -10,7 +10,7 @@ buildPythonPackage rec {
     owner = "jmcgeheeiv";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0rhbkcb5h2x8kmyxivr5jr1db2xvmpjdbsfjxl142qhfb29hr2hp";
+    sha256 = "1pww444ih4bf84a0jgl1r446mjywhlls890mnw76flx8maahlik1";
   };
 
   postPatch = ''
@@ -33,7 +33,8 @@ buildPythonPackage rec {
   checkPhase = ''
     export LC_ALL=en_US.UTF-8
     ${python.interpreter} -m pyfakefs.tests.all_tests
-    ${python.interpreter} -m pytest pyfakefs/tests/pytest_plugin_test.py
+    ${python.interpreter} -m pyfakefs.tests.all_tests_without_extra_packages
+    ${python.interpreter} -m pytest pyfakefs/tests/pytest/pytest_plugin_test.py
   '';
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/pygit2/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, lib, buildPythonPackage, fetchPypi, fetchpatch, isPyPy, libgit2, six, cffi }:
+{ stdenv, lib, buildPythonPackage, fetchPypi, fetchpatch, isPyPy, libgit2_0_27, six, cffi }:
 
 buildPythonPackage rec {
   pname = "pygit2";
@@ -10,7 +10,7 @@ buildPythonPackage rec {
   };
 
   preConfigure = lib.optionalString stdenv.isDarwin ''
-    export DYLD_LIBRARY_PATH="${libgit2}/lib"
+    export DYLD_LIBRARY_PATH="${libgit2_0_27}/lib"
   '';
 
   patches = [ (fetchpatch {
@@ -19,7 +19,7 @@ buildPythonPackage rec {
     sha256 = "18x1fpmywhjjr4lvakwmy34zpxfqi8pqqj48g1wcib39lh3s7l4f";
   }) ];
 
-  propagatedBuildInputs = [ libgit2 six ] ++ lib.optional (!isPyPy) cffi;
+  propagatedBuildInputs = [ libgit2_0_27 six ] ++ lib.optional (!isPyPy) cffi;
 
   preCheck = ''
     # disable tests that require networking

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "pyhomematic";
-  version = "0.1.53";
+  version = "0.1.54";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1crqdqbv7yqw2pasydy51ps048phbdn7s37xaba9npd1xm8g7jvh";
+    sha256 = "3c27f303e6a424229d2d5133af593c21f7d660bdf19d3d00641fbac08a6992c5";
   };
 
   # PyPI tarball does not include tests/ directory

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

@@ -0,0 +1,24 @@
+{ lib, buildPythonPackage, fetchFromGitHub }:
+
+buildPythonPackage rec {
+  pname = "pylev";
+  version = "1.3.0";
+
+  # No tests in PyPi tarball
+  src = fetchFromGitHub {
+    owner = "toastdriven";
+    repo = "pylev";
+    # Can't use a tag because it's missing
+    # https://github.com/toastdriven/pylev/issues/10
+    # rev = "v${version};
+    rev = "72e3d490515c3188e2acac9c15ea1b466f9ff938";
+    sha256 = "18dg1rfnqgfl6x4vafiq4la9d7f65xak19gcvngslq0bm1z6hyd8";
+  };
+
+  meta = with lib; {
+    homepage = https://github.com/toastdriven/pylev;
+    description = "A pure Python Levenshtein implementation that's not freaking GPL'd";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

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

@@ -4,6 +4,7 @@
 , six
 , pytest
 , hypothesis
+, pytestrunner
 }:
 
 buildPythonPackage rec {
@@ -16,11 +17,11 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [ six ];
-  buildInputs = [ pytest hypothesis ];
 
-  checkPhase = ''
+  checkInputs = [ pytestrunner pytest hypothesis ];
-    py.test
+
-  '';
+  # pytestrunner is only needed to run tests
+  patches = [ ./no-setup-requires-pytestrunner.patch ];
 
   meta = with stdenv.lib; {
     homepage = https://github.com/tobgu/pyrsistent/;

pkgs/development/python-modules/pyrsistent/no-setup-requires-pytestrunner.patch

@@ -0,0 +1,15 @@
+diff --git a/setup.py b/setup.py
+index 90a39a5..7bf444f 100644
+--- a/setup.py
++++ b/setup.py
+@@ -77,9 +77,8 @@ setup(
+         'Programming Language :: Python :: Implementation :: PyPy',
+     ],
+     test_suite='tests',
+-    tests_require=['pytest','hypothesis'],
++    tests_require=['pytest-runner', 'pytest','hypothesis'],
+     scripts=[],
+-    setup_requires=['pytest-runner'],
+     ext_modules=extensions,
+     cmdclass={'build_ext': custom_build_ext},
+     install_requires=['six'],

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

@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "scapy";
-  version = "2.4.0";
+  version = "2.4.2";
 
   disabled = isPyPy;
 
@@ -21,13 +21,16 @@ buildPythonPackage rec {
     owner = "secdev";
     repo = "scapy";
     rev = "v${version}";
-    sha256 = "0dw6kl1qi9bf3rbm79gb1h40ms8y0b5dbmpip841p2905d5r2isj";
+    sha256 = "03xzjklvc6y4d87k0rqpx5h112ld5nvgfldrbd8c4mx6f9mmd11n";
   };
 
   # TODO: Temporary workaround
-  patches = [ ./fix-version-1.patch ./fix-version-2.patch ];
+  patches = [ ./fix-version.patch ];
 
-  postPatch = lib.optionalString withManufDb ''
+  postPatch = ''
+    sed -i "s/NIXPKGS_SCAPY_VERSION/${version}/" \
+      setup.py scapy/__init__.py
+  '' + lib.optionalString withManufDb ''
     substituteInPlace scapy/data.py --replace "/opt/wireshark" "${wireshark}"
   '';
 

pkgs/development/python-modules/scapy/fix-version-1.patch

@@ -1,11 +0,0 @@
---- a/setup.py	2018-02-15 22:14:08.531591678 +0100
-+++ b/setup.py	2018-03-27 17:15:38.617315539 +0200
-@@ -47,7 +47,7 @@
- 
- setup(
-     name='scapy',
--    version=__import__('scapy').VERSION,
-+    version='2.4.0',
-     packages=[
-         'scapy',
-         'scapy/arch',

pkgs/development/python-modules/scapy/fix-version.patch

@@ -1,3 +1,14 @@
+--- a/setup.py	2018-02-15 22:14:08.531591678 +0100
++++ b/setup.py	2018-03-27 17:15:38.617315539 +0200
+@@ -47,7 +47,7 @@
+ 
+ setup(
+     name='scapy',
+-    version=__import__('scapy').VERSION,
++    version='NIXPKGS_SCAPY_VERSION',
+     packages=[
+         'scapy',
+         'scapy/arch',
 --- a/scapy/__init__.py	2018-03-27 17:38:52.706481269 +0200
 +++ b/scapy/__init__.py	2018-03-27 17:39:56.576688890 +0200
 @@ -82,9 +82,10 @@
@@ -5,10 +16,10 @@
                  return "git-archive.dev" + match.group(1)
              elif sha1:
 -                return "git-archive.dev" + sha1
-+                return '2.4.0'
++                return 'NIXPKGS_SCAPY_VERSION'
              else:
 -                return 'unknown.version'
-+                return '2.4.0'
++                return 'NIXPKGS_SCAPY_VERSION'
 +
  
  VERSION = _version()

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

@@ -1,6 +1,7 @@
 { stdenv
 , buildPythonPackage
 , fetchPypi
+, six
 }:
 
 buildPythonPackage rec {
@@ -12,6 +13,8 @@ buildPythonPackage rec {
     sha256 = "7d59ac4fdcb2c58037ebd4a9da5f9a49e3e034bf75b3f26d9fe48ba3d8806e6b";
   };
 
+  propagatedBuildInputs = [ six ];
+
   # No tests. Breaks when not disabling.
   doCheck = false;
 

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

@@ -3,6 +3,7 @@
 , fetchPypi
 , pytest
 , python
+, cython
 , cssutils
 , isPyPy
 }:
@@ -18,6 +19,17 @@ buildPythonPackage rec {
 
   checkInputs = [ pytest ];
   propagatedBuildInputs = [ cssutils ];
+  nativeBuildInputs = [
+    cython
+  ];
+
+  preBuild = ''
+    # Force cython to re-generate this file. If it is present, cython will
+    # think it is "up to date" even though it was generated with an older,
+    # incompatible version of cython. See
+    # https://github.com/Kozea/tinycss/issues/17.
+    rm tinycss/speedups.c
+  '';
 
   checkPhase = ''
     py.test $out/${python.sitePackages}

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

@@ -0,0 +1,29 @@
+{ lib, buildPythonPackage, fetchPypi, isPy27, isPy34
+, enum34, functools32, typing
+}:
+
+buildPythonPackage rec {
+  pname = "tomlkit";
+  version = "0.5.3";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1hjfzlb6y694pkadygcaq1n63di97pxgq2zpc74in1axc5166l6n";
+  };
+
+  propagatedBuildInputs =
+    lib.optionals isPy27 [ enum34 functools32 ]
+    ++ lib.optional (isPy27 || isPy34) typing;
+
+  # The Pypi tarball doesn't include tests, and the GitHub source isn't
+  # buildable until we bootstrap poetry, see
+  # https://github.com/NixOS/nixpkgs/pull/53599#discussion_r245855665
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/sdispater/tomlkit;
+    description = "Style-preserving TOML library for Python";
+    license = licenses.mit;
+    maintainers = with maintainers; [ jakewaksbaum ];
+  };
+}

pkgs/development/python-modules/xml2rfc/default.nix

@@ -1,4 +1,6 @@
-{ lib, fetchPypi, buildPythonPackage, intervaltree, pyflakes, requests, lxml }:
+{ lib, fetchPypi, buildPythonPackage, intervaltree, pyflakes, requests, lxml, google-i18n-address
+, pycountry, html5lib, six
+}:
 
 buildPythonPackage rec {
   pname = "xml2rfc";
@@ -9,7 +11,20 @@ buildPythonPackage rec {
     sha256 = "64609a2194d18c03e2348f1ea2fb97208b3455dfb76a16900143813aa61b6d3c";
   };
 
-  propagatedBuildInputs = [ intervaltree pyflakes requests lxml ];
+  propagatedBuildInputs = [
+    intervaltree
+    pyflakes
+    requests
+    lxml
+    google-i18n-address
+    pycountry
+    html5lib
+    six
+  ];
+
+  preCheck = ''
+    export HOME=$(mktemp -d)
+  '';
 
   meta = with lib; {
     description = "Tool generating IETF RFCs and drafts from XML sources";

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

@@ -15,6 +15,9 @@ buildPythonPackage rec {
   };
   propagatedBuildInputs = [ xorgserver ];
 
+  # See: https://github.com/cgoldberg/xvfbwrapper/issues/30
+  doCheck = false;
+
   checkInputs = [ mock ];
 
   meta = with stdenv.lib; {