Merge branch 'master' into staging-next

Larger rebuild, probably mainly haskell.
Hydra nixpkgs: ?compare=1503325

maintainers/maintainer-list.nix

@@ -68,6 +68,11 @@
     github = "abbradar";
     name = "Nikolay Amiantov";
   };
+  abhi18av = {
+    email = "abhi18av@gmail.com";
+    github = "abhi18av";
+    name = "Abhinav Sharma";
+  };
   abigailbuccaneer = {
     email = "abigailbuccaneer@gmail.com";
     github = "abigailbuccaneer";
@@ -4677,7 +4682,7 @@
     name = "Thomas Tuegel";
   };
   tv = {
-    email = "tv@shackspace.de";
+    email = "tv@krebsco.de";
     github = "4z3";
     name = "Tomislav Viljetić";
   };

nixos/modules/tasks/auto-upgrade.nix

@@ -78,7 +78,7 @@ let cfg = config.system.autoUpgrade; in
           HOME = "/root";
         } // config.networking.proxy.envVars;
 
-      path = [ pkgs.gnutar pkgs.xz.bin config.nix.package.out ];
+      path = [ pkgs.gnutar pkgs.xz.bin pkgs.gitMinimal config.nix.package.out ];
 
       script = ''
         ${config.system.build.nixos-rebuild}/bin/nixos-rebuild switch ${toString cfg.flags}

nixos/tests/all-tests.nix

@@ -142,6 +142,7 @@ in
   nat.firewall = handleTest ./nat.nix { withFirewall = true; };
   nat.firewall-conntrack = handleTest ./nat.nix { withFirewall = true; withConntrackHelpers = true; };
   nat.standalone = handleTest ./nat.nix { withFirewall = false; };
+  neo4j = handleTest ./neo4j.nix {};
   netdata = handleTest ./netdata.nix {};
   networking.networkd = handleTest ./networking.nix { networkd = true; };
   networking.scripted = handleTest ./networking.nix { networkd = false; };

nixos/tests/neo4j.nix

@@ -0,0 +1,20 @@
+import ./make-test.nix {
+  name = "neo4j";
+
+  nodes = {
+    master =
+      { ... }:
+
+      {
+        services.neo4j.enable = true;
+      };
+  };
+
+  testScript = ''
+    startAll;
+
+    $master->waitForUnit("neo4j");
+    $master->sleep(20); # Hopefully this is long enough!!
+    $master->succeed("curl http://localhost:7474/");
+  '';
+}

pkgs/applications/editors/android-studio/default.nix

@@ -13,14 +13,14 @@ let
     sha256Hash = "0dracganibnkyapn2pk2qqnxpwmii57371ycri4nccaci9v9pcjw";
   };
   betaVersion = {
-    version = "3.4.0.11"; # "Android Studio 3.4 Beta 2"
+    version = "3.4.0.12"; # "Android Studio 3.4 Beta 3"
-    build = "183.5240537";
+    build = "183.5256591";
-    sha256Hash = "0mv7ayqjkw97jzdifw1cdvjhnzygzkd2a9rc0h99fclhf2nii5yr";
+    sha256Hash = "1yab2sgabgk3wa3wrzv9z1dc2k7x0079v0mlwrp32jwx8r9byvcw";
   };
   latestVersion = { # canary & dev
-    version = "3.5.0.1"; # "Android Studio 3.5 Canary 2"
+    version = "3.5.0.2"; # "Android Studio 3.5 Canary 3"
-    build = "183.5240547";
+    build = "183.5256920";
-    sha256Hash = "0z52ig9v2w9i6bqiqpdvgcr6g6sgl8p5317jamg72d5csm9hgfx3";
+    sha256Hash = "09bd80ld21hq743xjacsq0nkxwl5xzr253p86n71n580yn4rgmlb";
   };
 in rec {
   # Old alias (TODO @primeos: Remove after 19.03 is branched off):

pkgs/applications/misc/calibre/default.nix

@@ -5,12 +5,12 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "3.38.1";
+  version = "3.39.1";
   name = "calibre-${version}";
 
   src = fetchurl {
     url = "https://download.calibre-ebook.com/${version}/${name}.tar.xz";
-    sha256 = "07fvpnabk17sfg81xn0bsnw36k45hawwz0fcz5cmp5qydm85ncv0";
+    sha256 = "08c1wsdn0giv9zfb6bis9bbrw687rci8fs26qsal8ijmjk55dfsh";
   };
 
   patches = [

pkgs/applications/misc/cool-retro-term/default.nix

@@ -2,14 +2,14 @@
 , qtquickcontrols, qtgraphicaleffects, qmake }:
 
 stdenv.mkDerivation rec {
-  version = "1.1.0";
+  version = "1.1.1";
   name = "cool-retro-term-${version}";
 
   src = fetchFromGitHub {
     owner = "Swordfish90";
     repo = "cool-retro-term";
     rev = version;
-    sha256 = "0gmigjpc19q7l94q4wzbrxh7cdb6zk3zscaijzwsz9364wsgzb47";
+    sha256 = "0mird4k88ml6y61hky2jynrjmnxl849fvhsr5jfdlnv0i7r5vwi5";
   };
 
   patchPhase = ''

pkgs/applications/networking/cluster/kube-router/default.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "kube-router-${version}";
-  version = "0.2.3";
+  version = "0.2.5";
   rev = "v${version}";
 
   goPackagePath = "github.com/cloudnativelabs/kube-router";
@@ -11,7 +11,7 @@ buildGoPackage rec {
     inherit rev;
     owner = "cloudnativelabs";
     repo = "kube-router";
-    sha256 = "1dsr76dq6sycwgh75glrcb4scv52lrrd0aivskhc7mwq30plafcj";
+    sha256 = "1j6q6kg4qj75v2mdy9ivvwq8mx9fpdf0w08959l8imrp5byd56wv";
   };
 
   buildFlagsArray = ''

pkgs/applications/networking/gns3/default.nix

@@ -2,8 +2,7 @@
 
 let
   stableVersion = "2.1.12";
-  # Currently there is no preview version.
+  previewVersion = "2.2.0a1";
-  previewVersion = stableVersion;
   addVersion = args:
     let version = if args.stable then stableVersion else previewVersion;
         branch = if args.stable then "stable" else "preview";
@@ -19,7 +18,7 @@ in {
   };
   guiPreview = mkGui {
     stable = false;
-    sha256Hash = guiSrcHash;
+    sha256Hash = "16jjgfbdi7b3349wrqalf40qcaqzw3d4vdjbwcy8dbqblg48hn5w";
   };
 
   serverStable = mkServer {
@@ -28,6 +27,6 @@ in {
   };
   serverPreview = mkServer {
     stable = false;
-    sha256Hash = serverSrcHash;
+    sha256Hash = "0bcsjljy947grfn3y9xyi3dbzdw5wkljq1nr66cqfkidx9f4fzni";
   };
 }

pkgs/applications/networking/gns3/gui.nix

@@ -20,7 +20,7 @@ in pythonPackages.buildPythonPackage rec {
     raven psutil jsonschema # tox for check
     # Runtime dependencies
     sip (pyqt5.override { withWebSockets = true; })
-  ];
+  ] ++ stdenv.lib.optional (!stable) pythonPackages.distro;
 
   doCheck = false; # Failing
 

pkgs/applications/networking/gns3/server.nix

@@ -3,7 +3,7 @@
 { stdenv, python36, fetchFromGitHub }:
 
 let
-  python = python36.override {
+  python = if stable then python36.override {
     packageOverrides = self: super: {
       async-timeout = super.async-timeout.overridePythonAttrs (oldAttrs: rec {
         version = "2.0.1";
@@ -31,7 +31,7 @@ let
           ++ stdenv.lib.optional (pythonOlder "3.5") typing;
       });
     };
-  };
+  } else python36;
 
 in python.pkgs.buildPythonPackage {
   pname = "gns3-server";
@@ -48,7 +48,7 @@ in python.pkgs.buildPythonPackage {
     aiohttp-cors yarl aiohttp multidict
     jinja2 psutil zipstream raven jsonschema typing
     (python.pkgs.callPackage ../../../development/python-modules/prompt_toolkit/1.nix {})
-  ];
+  ] ++ stdenv.lib.optional (!stable) python.pkgs.distro;
 
   # Requires network access
   doCheck = false;

pkgs/applications/networking/instant-messengers/telegram/tdesktop/default.nix

@@ -4,11 +4,11 @@ let
   mkTelegram = args: qt5.callPackage (import ./generic.nix args) { };
   stableVersion = {
     stable = true;
-    version = "1.5.8";
+    version = "1.5.11";
-    sha256Hash = "0sl4p4a7fyh68g01rddiy719lyr321cjar78b3c732zxfj8lxvkb";
+    sha256Hash = "09blyzs6mrmrrmjcfia9pa35mfv4zfc9mrqc36hqqcchmg54kx6w";
     # svn log svn://svn.archlinux.org/community/telegram-desktop/trunk
-    archPatchesRevision = "415526";
+    archPatchesRevision = "429149";
-    archPatchesHash = "1lfzws90ab0vajhm5r64gyyqqc1g6a2ay0a1vkp0ah1iw5jh11ik";
+    archPatchesHash = "1ylpi9kb6hk27x9wmna4ing8vzn9b7247iya91pyxxrpxrcrhpli";
   };
 in {
   stable = mkTelegram stableVersion;

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

@@ -13,11 +13,11 @@ assert pulseaudioSupport -> libpulseaudio != null;
 let
   inherit (stdenv.lib) concatStringsSep makeBinPath optional;
 
-  version = "2.6.149990.1216";
+  version = "2.7.162522.0121";
   srcs = {
     x86_64-linux = fetchurl {
       url = "https://zoom.us/client/${version}/zoom_x86_64.tar.xz";
-      sha256 = "0bs5kx2601lwwr9lgdd3hlbrrwsf0dai766zrca907dl400pmzyd";
+      sha256 = "01i4g4kmawk3mclifh4bwcqpdnbvrz0sz49b6l33n0k5ysky20r1";
     };
   };
 
@@ -49,7 +49,6 @@ in stdenv.mkDerivation {
       files = concatStringsSep " " [
         "*.pcm"
         "*.png"
-        "ZXMPPROOT.cer"
         "ZoomLauncher"
         "config-dump.sh"
         "timezones"

pkgs/applications/networking/mailreaders/notmuch/default.nix

@@ -12,7 +12,7 @@
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
-  version = "0.28";
+  version = "0.28.1";
   name = "notmuch-${version}";
 
   passthru = {
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://notmuchmail.org/releases/${name}.tar.gz";
-    sha256 = "0dqarmjc8544m2w7bqrqmvsfy55fw82707z3lz9cql8nr777bjmc";
+    sha256 = "0mcsfkrp6mpy374m5rwwgm9md8qzvwa3s4rbzid4cnkx2cwfj4fi";
   };
 
   nativeBuildInputs = [ pkgconfig ];

pkgs/development/compilers/ghcjs-ng/8.2/git.json

@@ -1,6 +0,0 @@
-{
-  "url": "https://github.com/ghcjs/ghcjs",
-  "rev": "0cff73c3ee13b464adba90f308b77751c75b9f26",
-  "sha256": "1shg34zi6ryaihar62qdkkalv8dsrsqbv58jzkhk9in38sdfkjxv",
-  "fetchSubmodules": true
-}

pkgs/development/compilers/ghcjs-ng/8.4/dep-overrides.nix

@@ -2,6 +2,8 @@
 
 let inherit (haskellLib) dontCheck doJailbreak;
 in self: super: {
-  haddock-library-ghcjs = dontCheck super.haddock-library-ghcjs;
+  haddock-library-ghcjs = doJailbreak (dontCheck super.haddock-library-ghcjs);
   haddock-api-ghcjs = doJailbreak super.haddock-api-ghcjs;
+
+  template-haskell-ghcjs = doJailbreak super.template-haskell-ghcjs;
 }

pkgs/development/compilers/ghcjs-ng/8.6/dep-overrides.nix

@@ -0,0 +1,7 @@
+{ haskellLib }:
+
+let inherit (haskellLib) dontCheck doJailbreak dontHaddock;
+in self: super: {
+  haddock-library-ghcjs = doJailbreak super.haddock-library-ghcjs;
+  haddock-api-ghcjs = doJailbreak (dontHaddock super.haddock-api-ghcjs);
+}

pkgs/development/compilers/ghcjs-ng/8.6/git.json

@@ -0,0 +1,6 @@
+{
+  "url": "https://github.com/ghcjs/ghcjs",
+  "rev": "75c61af32d73def4409d1fe7b64659c1d28cd075",
+  "sha256": "18pixn6xdz6qp941yhxfnmwi463jnpskmg473lv07vvgy4hpgjhj",
+  "fetchSubmodules": true
+}

pkgs/development/compilers/ghcjs-ng/8.6/stage0.nix

@@ -20,7 +20,7 @@
     }:
     mkDerivation {
       pname = "ghcjs";
-      version = "8.2.0.1";
+      version = "8.6.0.1";
       src = configuredSrc + /.;
       isLibrary = true;
       isExecutable = true;
@@ -60,17 +60,17 @@
 
   ghc-api-ghcjs = callPackage
     ({ mkDerivation, array, base, binary, bytestring, containers
-    , deepseq, directory, filepath, ghc-boot, ghc-boot-th, ghci-ghcjs
+    , deepseq, directory, filepath, ghc-boot, ghc-boot-th, ghc-heap
-    , hoopl, hpc, process, stdenv, template-haskell-ghcjs, terminfo
+    , ghci-ghcjs, hpc, process, stdenv, template-haskell-ghcjs
-    , time, transformers, unix
+    , terminfo, time, transformers, unix
     }:
     mkDerivation {
       pname = "ghc-api-ghcjs";
-      version = "8.2.2";
+      version = "8.6.2";
       src = configuredSrc + /lib/ghc-api-ghcjs;
       libraryHaskellDepends = [
         array base binary bytestring containers deepseq directory filepath
-        ghc-boot ghc-boot-th ghci-ghcjs hoopl hpc process
+        ghc-boot ghc-boot-th ghc-heap ghci-ghcjs hpc process
         template-haskell-ghcjs terminfo time transformers unix
       ];
       homepage = "http://www.haskell.org/ghc/";
@@ -80,16 +80,16 @@
 
   ghci-ghcjs = callPackage
     ({ mkDerivation, array, base, binary, bytestring, containers
-    , deepseq, filepath, ghc-boot, ghc-boot-th, stdenv
+    , deepseq, filepath, ghc-boot, ghc-boot-th, ghc-heap, stdenv
     , template-haskell-ghcjs, transformers, unix
     }:
     mkDerivation {
       pname = "ghci-ghcjs";
-      version = "8.2.2";
+      version = "8.6.1";
       src = configuredSrc + /lib/ghci-ghcjs;
       libraryHaskellDepends = [
         array base binary bytestring containers deepseq filepath ghc-boot
-        ghc-boot-th template-haskell-ghcjs transformers unix
+        ghc-boot-th ghc-heap template-haskell-ghcjs transformers unix
       ];
       description = "The library supporting GHC's interactive interpreter (customized for GHCJS)";
       license = stdenv.lib.licenses.bsd3;
@@ -119,7 +119,7 @@
     }:
     mkDerivation {
       pname = "haddock-api-ghcjs";
-      version = "2.18.1";
+      version = "2.20.0";
       src = configuredSrc + /lib/haddock-api-ghcjs;
       enableSeparateDataOutput = true;
       libraryHaskellDepends = [
@@ -128,25 +128,33 @@
         xhtml
       ];
       testHaskellDepends = [
-        base containers ghc-api-ghcjs hspec QuickCheck
+        array base bytestring Cabal containers deepseq directory filepath
+        ghc-api-ghcjs ghc-boot ghc-paths haddock-library-ghcjs hspec
+        QuickCheck transformers xhtml
       ];
       testToolDepends = [ hspec-discover ];
       homepage = "http://www.haskell.org/haddock/";
-      description = "A documentation-generation tool for Haskell libraries (customized for GHCJS)";
+      description = "A documentation-generation tool for Haskell libraries";
       license = stdenv.lib.licenses.bsd3;
     }) {};
 
   haddock-library-ghcjs = callPackage
-    ({ mkDerivation, base, base-compat, bytestring, deepseq, hspec
+    ({ mkDerivation, base, base-compat, bytestring, containers, deepseq
-    , hspec-discover, QuickCheck, stdenv, transformers
+    , directory, filepath, haddock-library, hspec, hspec-discover
+    , optparse-applicative, parsec, QuickCheck, stdenv, text
+    , transformers, tree-diff
     }:
     mkDerivation {
       pname = "haddock-library-ghcjs";
-      version = "1.4.4";
+      version = "1.6.0";
       src = configuredSrc + /lib/haddock-library-ghcjs;
-      libraryHaskellDepends = [ base bytestring deepseq transformers ];
+      libraryHaskellDepends = [
+        base bytestring containers parsec text transformers
+      ];
       testHaskellDepends = [
-        base base-compat bytestring deepseq hspec QuickCheck transformers
+        base base-compat bytestring containers deepseq directory filepath
+        haddock-library hspec optparse-applicative parsec QuickCheck text
+        transformers tree-diff
       ];
       testToolDepends = [ hspec-discover ];
       homepage = "http://www.haskell.org/haddock/";
@@ -158,7 +166,7 @@
     ({ mkDerivation, base, ghc-boot-th, pretty, stdenv }:
     mkDerivation {
       pname = "template-haskell-ghcjs";
-      version = "2.12.0.0";
+      version = "2.14.0.0";
       src = configuredSrc + /lib/template-haskell-ghcjs;
       libraryHaskellDepends = [ base ghc-boot-th pretty ];
       description = "Support library for Template Haskell (customized for GHCJS)";

pkgs/development/compilers/ghcjs-ng/configured-ghcjs-src.nix

@@ -43,6 +43,8 @@ runCommand "configured-ghcjs-src" {
   # TODO: How to actually fix this?
   # Seems to work fine and produce the right files.
   touch ghc/includes/ghcautoconf.h
+  mkdir -p ghc/compiler/vectorise
+  mkdir -p ghc/utils/haddock/haddock-library/vendor
 
   patchShebangs .
   ./utils/makePackages.sh copy

pkgs/development/compilers/ghcjs-ng/default.nix

@@ -104,7 +104,5 @@ in stdenv.mkDerivation {
     inherit passthru;
 
     meta.platforms = passthru.bootPkgs.ghc.meta.platforms;
-    meta.hydraPlatforms = [];
+    meta.maintainers = [lib.maintainers.elvishjerricco];
-    meta.broken = true;  # does not compile: https://hydra.nixos.org/build/88052615
-
   }

pkgs/development/haskell-modules/configuration-common.nix

@@ -85,7 +85,7 @@ self: super: {
       name = "git-annex-${super.git-annex.version}-src";
       url = "git://git-annex.branchable.com/";
       rev = "refs/tags/" + super.git-annex.version;
-      sha256 = "0vww2qf94a6dg46mynkgpk0lh3x12vvfby3flqymi4wfrx1fif1k";
+      sha256 = "06385r9rlncrrmzdfl8q600bw6plbvkmkwgl3llg595xrm711a97";
     };
   }).override {
     dbus = if pkgs.stdenv.isLinux then self.dbus else null;
@@ -935,7 +935,12 @@ self: super: {
   # aarch64 and armv7l fixes.
   happy = if (pkgs.stdenv.hostPlatform.isAarch32 || pkgs.stdenv.hostPlatform.isAarch64) then dontCheck super.happy else super.happy; # Similar to https://ghc.haskell.org/trac/ghc/ticket/13062
   hashable = if (pkgs.stdenv.hostPlatform.isAarch32 || pkgs.stdenv.hostPlatform.isAarch64) then dontCheck super.hashable else super.hashable; # https://github.com/tibbe/hashable/issues/95
-  servant-docs = if (pkgs.stdenv.hostPlatform.isAarch32 || pkgs.stdenv.hostPlatform.isAarch64) then dontCheck super.servant-docs else super.servant-docs;
+  servant-docs =
+    let
+      f = if (pkgs.stdenv.hostPlatform.isAarch32 || pkgs.stdenv.hostPlatform.isAarch64)
+          then dontCheck
+          else pkgs.lib.id;
+    in doJailbreak (f super.servant-docs); # jailbreak tasty < 1.2 until servant-docs > 0.11.3 is on hackage.
   swagger2 = if (pkgs.stdenv.hostPlatform.isAarch32 || pkgs.stdenv.hostPlatform.isAarch64) then dontHaddock (dontCheck super.swagger2) else super.swagger2;
 
   # requires a release including https://github.com/haskell-servant/servant-swagger/commit/249530d9f85fe76dfb18b100542f75a27e6a3079
@@ -1182,4 +1187,16 @@ self: super: {
   hlint = super.hlint.overrideScope (self: super: { haskell-src-exts = self.haskell-src-exts_1_21_0; });
   hoogle = super.hoogle.overrideScope (self: super: { haskell-src-exts = self.haskell-src-exts_1_21_0; });
 
+  # Jailbreak tasty < 1.2: https://github.com/phadej/tdigest/issues/30
+  tdigest = doJailbreak super.tdigest; # until tdigest > 0.2.1
+
+  # These patches contain fixes for 8.6 that should be safe for
+  # earlier versions, but we need the relaxed version bounds in GHC
+  # 8.4 builds. beam needs to release a round of updates that relax
+  # bounds and include the 8.6 fixes:
+  # https://github.com/tathougies/beam/issues/315
+  beam-core = appendPatch super.beam-core ./patches/beam-core-fix-ghc-8.6.x-build.patch;
+  beam-migrate = appendPatch super.beam-migrate ./patches/beam-migrate-fix-ghc-8.6.x-build.patch;
+  beam-postgres = appendPatch super.beam-postgres ./patches/beam-postgres-fix-ghc-8.6.x-build.patch;
+  beam-sqlite = appendPatch super.beam-sqlite ./patches/beam-sqlite-fix-ghc-8.6.x-build.patch;
 } // import ./configuration-tensorflow.nix {inherit pkgs haskellLib;} self super

pkgs/development/haskell-modules/configuration-ghc-8.4.x.nix

@@ -76,4 +76,7 @@ self: super: {
     haddock-library = dontHaddock (dontCheck self.haddock-library_1_5_0_1);
   }));
 
+  # cabal2nix doesn't list this because of a conditional on the GHC version.
+  aeson = addBuildDepend super.aeson self.contravariant;
+
 }

pkgs/development/haskell-modules/configuration-ghc-head.nix

@@ -35,7 +35,6 @@ self: super: {
   integer-gmp = null;
   libiserv = null;
   mtl = null;
-  parallel = null;
   parsec = null;
   pretty = null;
   process = null;

pkgs/development/haskell-modules/generic-builder.nix

@@ -377,6 +377,10 @@ stdenv.mkDerivation ({
     runHook postHaddock
   '';
 
+  # The scary sed expression handles two cases in v2.5 Cabal's package configs:
+  # 1. 'id:    short-name-0.0.1-9yvw8HF06tiAXuxm5U8KjO'
+  # 2. 'id:\n
+  #         very-long-descriptive-useful-name-0.0.1-9yvw8HF06tiAXuxm5U8KjO'
   installPhase = ''
     runHook preInstall
 
@@ -391,7 +395,7 @@ stdenv.mkDerivation ({
         rmdir "$packageConfFile"
       fi
       for packageConfFile in "$packageConfDir/"*; do
-        local pkgId=$( ${gnused}/bin/sed -n -e 's|^id:[ ]\+||p' $packageConfFile )
+        local pkgId=$( ${gnused}/bin/sed -n -e ':a' -e '/^id:$/N; s/id:\n[ ]*\([^\n]*\).*$/\1/p; s/id:[ ]*\([^\n]*\)$/\1/p; ta' $packageConfFile )
         mv $packageConfFile $packageConfDir/$pkgId.conf
       done
 

pkgs/development/haskell-modules/patches/beam-core-fix-ghc-8.6.x-build.patch

@@ -0,0 +1,72 @@
+diff --git a/beam-core/Database/Beam/Backend/SQL.hs b/beam-core/Database/Beam/Backend/SQL.hs
+index e2cd37d0..6f9db126 100644
+--- a/Database/Beam/Backend/SQL.hs
++++ b/Database/Beam/Backend/SQL.hs
+@@ -10,6 +10,7 @@
+ import Database.Beam.Backend.Types
+ 
+ import Control.Monad.IO.Class
++import Control.Monad.Fail (MonadFail)
+ 
+ -- * MonadBeam class
+ 
+@@ -29,7 +30,7 @@
+ --   strategies. More complicated strategies (for example, Postgres's @COPY@)
+ --   are supported in individual backends. See the documentation of those
+ --   backends for more details.
+-class (BeamBackend be, Monad m, MonadIO m, Sql92SanityCheck syntax) =>
++class (BeamBackend be, Monad m, MonadIO m, MonadFail m, Sql92SanityCheck syntax) =>
+   MonadBeam syntax be handle m | m -> syntax be handle where
+ 
+   {-# MINIMAL withDatabaseDebug, runReturningMany #-}
+diff --git a/Database/Beam/Backend/SQL/Builder.hs b/Database/Beam/Backend/SQL/Builder.hs
+index 9e734036..e9849912 100644
+--- a/Database/Beam/Backend/SQL/Builder.hs
++++ b/Database/Beam/Backend/SQL/Builder.hs
+@@ -33,6 +33,7 @@
+ import           Data.Hashable
+ import           Data.Int
+ import           Data.String
++import qualified Control.Monad.Fail as Fail
+ #if !MIN_VERSION_base(4, 11, 0)
+ import           Data.Semigroup
+ #endif
+@@ -507,8 +508,10 @@
+   type BackendFromField SqlSyntaxBackend = Trivial
+ 
+ newtype SqlSyntaxM a = SqlSyntaxM (IO a)
+-  deriving (Applicative, Functor, Monad, MonadIO)
++  deriving (Applicative, Functor, Monad, MonadIO, Fail.MonadFail)
+ 
+ instance MonadBeam SqlSyntaxBuilder SqlSyntaxBackend SqlSyntaxBackend SqlSyntaxM where
+-  withDatabaseDebug _ _ _ = fail "absurd"
+-  runReturningMany _ _ = fail "absurd"
++  withDatabaseDebug _ _ _ = Fail.fail "absurd"
++  runReturningMany _ _ = Fail.fail "absurd"
++
++
+diff --git a/Database/Beam/Schema/Lenses.hs b/Database/Beam/Schema/Lenses.hs
+index b21dddb6..5df0654c 100644
+--- a/Database/Beam/Schema/Lenses.hs
++++ b/Database/Beam/Schema/Lenses.hs
+@@ -1,4 +1,5 @@
+ {-# LANGUAGE PolyKinds #-}
++{-# LANGUAGE UndecidableInstances #-}
+ module Database.Beam.Schema.Lenses
+     ( tableLenses
+     , TableLens(..)
+diff --git a/beam-core.cabal b/beam-core.cabal
+index 4bf4ffd9..251d4d85 100644
+--- a/beam-core.cabal
++++ b/beam-core.cabal
+@@ -64,8 +64,8 @@
+                        time         >=1.6     && <1.10,
+                        hashable     >=1.1     && <1.3,
+                        network-uri  >=2.6     && <2.7,
+-                       containers   >=0.5     && <0.6,
+-                       vector-sized >=0.5     && <1.1,
++                       containers   >=0.5     && <0.7,
++                       vector-sized >=0.5     && <1.3,
+                        tagged       >=0.8     && <0.9
+   Default-language:    Haskell2010
+   default-extensions:  ScopedTypeVariables, OverloadedStrings, GADTs, RecursiveDo, FlexibleInstances, FlexibleContexts, TypeFamilies,

pkgs/development/haskell-modules/patches/beam-migrate-fix-ghc-8.6.x-build.patch

@@ -0,0 +1,29 @@
+diff --git a/Database/Beam/Migrate/Generics/Types.hs b/Database/Beam/Migrate/Generics/Types.hs
+index 553e208b..0cf9b2c8 100644
+--- a/Database/Beam/Migrate/Generics/Types.hs
++++ b/Database/Beam/Migrate/Generics/Types.hs
+@@ -1,3 +1,5 @@
++{-# LANGUAGE UndecidableInstances #-}
++
+ module Database.Beam.Migrate.Generics.Types where
+ 
+ import           Database.Beam.Migrate.Types
+diff --git a/beam-migrate.cabal b/beam-migrate.cabal
+index f53b280d..9cf3722c 100644
+--- a/beam-migrate.cabal
++++ b/beam-migrate.cabal
+@@ -69,13 +69,12 @@ library
+                        mtl                  >=2.2     && <2.3,
+                        scientific           >=0.3     && <0.4,
+                        vector               >=0.11    && <0.13,
+-                       containers           >=0.5     && <0.6,
+                        unordered-containers >=0.2     && <0.3,
+                        hashable             >=1.2     && <1.3,
+                        parallel             >=3.2     && <3.3,
+                        deepseq              >=1.4     && <1.5,
+                        ghc-prim             >=0.5     && <0.6,
+-                       containers           >=0.5     && <0.6,
++                       containers           >=0.5     && <0.7,
+                        haskell-src-exts     >=1.18    && <1.21,
+                        pretty               >=1.1     && <1.2,
+                        dependent-map        >=0.2     && <0.3,

pkgs/development/haskell-modules/patches/beam-postgres-fix-ghc-8.6.x-build.patch

@@ -0,0 +1,45 @@
+diff --git a/Database/Beam/Postgres/Connection.hs b/Database/Beam/Postgres/Connection.hs
+index 433f55b9..5836c53d 100644
+--- a/Database/Beam/Postgres/Connection.hs
++++ b/Database/Beam/Postgres/Connection.hs
+@@ -52,6 +52,8 @@ import qualified Database.PostgreSQL.Simple.Types as Pg (Null(..), Query(..))
+ 
+ import           Control.Monad.Reader
+ import           Control.Monad.State
++import           Control.Monad.Fail (MonadFail)
++import qualified Control.Monad.Fail as Fail
+ 
+ import           Data.ByteString (ByteString)
+ import           Data.ByteString.Builder (toLazyByteString, byteString)
+@@ -302,6 +304,9 @@ deriving instance Functor PgF
+ newtype Pg a = Pg { runPg :: F PgF a }
+     deriving (Monad, Applicative, Functor, MonadFree PgF)
+ 
++instance MonadFail Pg where
++    fail e = fail $ "Internal Error with: " <> show e
++
+ instance MonadIO Pg where
+     liftIO x = liftF (PgLiftIO x id)
+ 
+diff --git a/beam-postgres.cabal b/beam-postgres.cabal
+index e14b84f5..d29a5b67 100644
+--- a/beam-postgres.cabal
++++ b/beam-postgres.cabal
+@@ -31,7 +31,7 @@ library
+                       beam-migrate         >=0.3  && <0.4,
+ 
+                       postgresql-libpq     >=0.8  && <0.10,
+-                      postgresql-simple    >=0.5  && <0.6,
++                      postgresql-simple    >=0.5  && <0.7,
+ 
+                       text                 >=1.0  && <1.3,
+                       bytestring           >=0.10 && <0.11,
+@@ -38,7 +38,7 @@ library
+ 
+                       hashable             >=1.1  && <1.3,
+                       lifted-base          >=0.2  && <0.3,
+-                      free                 >=4.12 && <5.1,
++                      free                 >=4.12 && <5.2,
+                       time                 >=1.6  && <1.10,
+                       monad-control        >=1.0  && <1.1,
+                       mtl                  >=2.1  && <2.3,

pkgs/development/haskell-modules/patches/beam-sqlite-fix-ghc-8.6.x-build.patch

@@ -0,0 +1,21 @@
+diff --git a/Database/Beam/Sqlite/Connection.hs b/Database/Beam/Sqlite/Connection.hs
+index f034b272..4e459ea3 100644
+--- a/Database/Beam/Sqlite/Connection.hs
++++ b/Database/Beam/Sqlite/Connection.hs
+@@ -37,6 +37,7 @@ import           Database.SQLite.Simple.Types (Null)
+ 
+ import           Control.Exception (bracket_, onException, mask)
+ import           Control.Monad (forM_, replicateM_)
++import           Control.Monad.Fail (MonadFail)
+ import           Control.Monad.Free.Church
+ import           Control.Monad.IO.Class (MonadIO(..))
+ import           Control.Monad.Identity (Identity)
+@@ -143,7 +144,7 @@ newtype SqliteM a
+   { runSqliteM :: ReaderT (String -> IO (), Connection) IO a
+     -- ^ Run an IO action with access to a SQLite connection and a debug logging
+     -- function, called or each query submitted on the connection.
+-  } deriving (Monad, Functor, Applicative, MonadIO)
++  } deriving (Monad, Functor, Applicative, MonadIO, MonadFail)
+ 
+ newtype BeamSqliteParams = BeamSqliteParams [SQLData]
+ instance ToRow BeamSqliteParams where

pkgs/development/interpreters/racket/default.nix

@@ -101,5 +101,6 @@ stdenv.mkDerivation rec {
     license = licenses.lgpl3;
     maintainers = with maintainers; [ kkallio henrytill vrthra ];
     platforms = [ "x86_64-darwin" "x86_64-linux" ];
+    broken = stdenv.isDarwin; # No support yet for setting FFI lookup path
   };
 }

pkgs/development/interpreters/racket/minimal.nix

@@ -15,5 +15,6 @@ racket.overrideAttrs (oldAttrs: rec {
       and the pkg library are still bundled.
     '';
     platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" ];
+    broken = false; # Minimal build does not require working FFI
   };
 })

pkgs/development/libraries/ftgl/default.nix

@@ -1,4 +1,4 @@
-{stdenv, fetchurl, freetype, libGLU_combined}:
+{ stdenv, fetchurl, freetype, libGLU_combined, OpenGL }:
 
 let
   name = "ftgl-2.1.3-rc5";
@@ -11,7 +11,12 @@ stdenv.mkDerivation {
     sha256 = "0nsn4s6vnv5xcgxcw6q031amvh2zfj2smy1r5mbnjj2548hxcn2l";
   };
 
-  buildInputs = [ freetype libGLU_combined ];
+  buildInputs = [ freetype ]
+    ++ (if stdenv.isDarwin then
+      [ OpenGL ]
+    else
+      [ libGLU_combined ])
+    ;
 
   enableParallelBuilding = true;
 

pkgs/development/libraries/zeitgeist/default.nix

@@ -5,22 +5,22 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.1";
+  pname = "zeitgeist";
-  name = "zeitgeist-${version}";
+  version = "1.0.2";
 
   outputs = [ "out" "lib" "dev" "man" ] ++ stdenv.lib.optional pythonSupport "py";
 
   src = fetchFromGitLab {
     domain = "gitlab.freedesktop.org";
-    owner = "zeitgeist";
+    owner = pname;
-    repo = "zeitgeist";
+    repo = pname;
     rev = "v${version}";
-    sha256 = "1lgqcqr5h9ba751b7ajp7h2w1bb5qza2w3k1f95j3ab15p7q0q44";
+    sha256 = "0ig3d3j1n0ghaxsgfww6g2hhcdwx8cljwwfmp9jk1nrvkxd6rnmv";
   };
 
   preConfigure = "NOCONFIGURE=1 ./autogen.sh";
 
-  configureFlags = [ "--with-session-bus-services-dir=$(out)/share/dbus-1/services" ];
+  configureFlags = [ "--with-session-bus-services-dir=${placeholder ''out''}/share/dbus-1/services" ];
 
   nativeBuildInputs = [
     autoconf automake libtool pkgconfig gettext gobject-introspection vala python2Packages.python
@@ -42,8 +42,8 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "A service which logs the users's activities and events";
-    homepage = http://zeitgeist.freedesktop.org/;
+    homepage = https://zeitgeist.freedesktop.org/;
-    maintainers = with maintainers; [ lethalman ];
+    maintainers = with maintainers; [ lethalman worldofpeace ];
     license = licenses.gpl2;
     platforms = platforms.linux;
   };

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

@@ -0,0 +1,30 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "filetype";
+  version = "1.0.2";
+
+  # No tests in PyPI tarball
+  # See https://github.com/h2non/filetype.py/pull/33
+  src = fetchFromGitHub {
+    owner = "h2non";
+    repo = "filetype.py";
+    rev = "v${version}";
+    sha256 = "000gl3q2cadfnmqnbxg31ppc3ak8blzb4nfn75faxbp7b6r5qgr2";
+  };
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover
+  '';
+
+  meta = with lib; {
+    description = "Infer file type and MIME type of any file/buffer";
+    homepage = https://github.com/h2non/filetype.py;
+    license = licenses.mit;
+    maintainers = with maintainers; [ dotlambda ];
+  };
+}

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

@@ -7,25 +7,22 @@
 
 buildPythonPackage rec {
   pname = "grammalecte";
-  version = "0.6.1";
+  version = "0.6.5";
 
   src = fetchurl {
     url = "http://www.dicollecte.org/grammalecte/zip/Grammalecte-fr-v${version}.zip";
-    sha256 = "0y2ck6pkd2p3cbjlxxvz3x5rnbg3ghfx97n13302rnab66cy4zkh";
+    sha256 = "11byjs3ggdhia5f4vyfqfvbbczsfqimll98h98g7hlsrm7vrifb0";
   };
 
   propagatedBuildInputs = [ bottle ];
 
   preBuild = "cd ..";
-  postInstall = ''
-    rm $out/bin/bottle.py
-  '';
 
   disabled = !isPy3k;
 
   meta = {
     description = "Grammalecte is an open source grammar checker for the French language";
-    homepage = https://dicollecte.org/grammalecte/;
+    homepage = https://grammalecte.net;
     license = with lib.licenses; [ gpl3 ];
     maintainers = with lib.maintainers; [ apeyroux ];
   };

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

@@ -0,0 +1,35 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, nose
+, coverage
+}:
+
+buildPythonPackage rec {
+  pname = "isbnlib";
+  version = "3.9.4";
+
+  # PyPI tarball is missing LICENSE file
+  # See https://github.com/xlcnd/isbnlib/pull/53
+  src = fetchFromGitHub {
+    owner = "xlcnd";
+    repo = "isbnlib";
+    rev = "v${version}";
+    sha256 = "0gc0k5khf34b4zz56a9zc3rscdhj3bx849lbzgmzpji30sbyy1fh";
+  };
+
+  checkInputs = [
+    nose
+    coverage
+  ];
+
+  # requires network connection
+  doCheck = false;
+
+  meta = with lib; {
+    description = "Extract, clean, transform, hyphenate and metadata for ISBNs";
+    homepage = https://github.com/xlcnd/isbnlib;
+    license = licenses.lgpl3;
+    maintainers = with maintainers; [ dotlambda ];
+  };
+}

pkgs/development/python-modules/keras-preprocessing/default.nix

@@ -1,24 +1,32 @@
-{ lib, buildPythonPackage, fetchPypi, numpy, scipy, six }:
+{ lib, buildPythonPackage, fetchPypi, numpy, six, scipy, pillow, pytest, Keras }:
 
 buildPythonPackage rec {
   pname = "Keras_Preprocessing";
-  version = "1.0.5";
+  version = "1.0.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754";
+    sha256 = "6e669aa713727f0bc08f756616f64e0dfa75d822226cfc0dcf33297ab05cef7d";
   };
 
-  # Cyclic dependency: keras-preprocessing requires keras, which requires keras-preprocessing
+  propagatedBuildInputs = [
-  postPatch = ''
+    # required
-    sed -i "s/keras>=[^']*//" setup.py
+    numpy six
+    # optional
+    scipy pillow
+  ];
+
+  checkInputs = [
+    pytest Keras
+  ];
+
+  checkPhase = ''
+    py.test tests/
   '';
 
-  # No tests in PyPI tarball
+  # Cyclic dependency: keras-preprocessing's tests require Keras, which requires keras-preprocessing
   doCheck = false;
 
-  propagatedBuildInputs = [ numpy scipy six ];
-
   meta = with lib; {
     description = "Easy data preprocessing and data augmentation for deep learning models";
     homepage = https://github.com/keras-team/keras-preprocessing;

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

@@ -25,14 +25,6 @@ buildPythonPackage rec {
     keras-applications keras-preprocessing
   ];
 
-  # Keras 2.2.2 expects older versions of keras_applications
-  # and keras_preprocessing. These substitutions can be removed
-  # for for the next Keras release.
-  postPatch = ''
-    substituteInPlace setup.py --replace "keras_applications==1.0.4" "keras_applications==1.0.5"
-    substituteInPlace setup.py --replace "keras_preprocessing==1.0.2" "keras_preprocessing==1.0.3"
-  '';
-
   # Couldn't get tests working
   doCheck = false;
 

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

@@ -2,14 +2,14 @@
 
 buildPythonPackage rec {
   pname = "keyutils";
-  version = "0.5";
+  version = "0.6";
 
   # github version comes bundled with tests
   src = fetchFromGitHub {
     owner = "sassoftware";
     repo = "python-keyutils";
-    rev = "v${version}";
+    rev = version;
-    sha256 = "1gga60w8sb3r5bxa0bfp7d7wzg6s3db5y7aizr14p2pvp92d8bdi";
+    sha256 = "0pfqfr5xqgsqkxzrmj8xl2glyl4nbq0irs0k6ik7iy3gd3mxf5g1";
   };
 
   buildInputs = [ keyutils ];

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

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, makeWrapper, jre }:
 
 stdenv.mkDerivation rec {
-  version = "8.16";
+  version = "8.17";
   name = "checkstyle-${version}";
 
   src = fetchurl {
     url = "https://github.com/checkstyle/checkstyle/releases/download/checkstyle-${version}/checkstyle-${version}-all.jar";
-    sha256 = "1044imm1pmn4fb0bzg4k44qm1hwwsyf7l7lbnlrznbln7ymdy5ki";
+    sha256 = "10i285kzbma9pny0vlm8wglxsbqliqrhig6n9rj2nv13x5i53ifj";
   };
 
   nativeBuildInputs = [ makeWrapper ];

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

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "mill-${version}";
-  version = "0.3.5";
+  version = "0.3.6";
 
   src = fetchurl {
     url = "https://github.com/lihaoyi/mill/releases/download/${version}/${version}";
-    sha256 = "19ka81f6vjr85gd8cadn0fv0i0qcdspx2skslfksklxdxs2gasf8";
+    sha256 = "1dal08l96a5w8g27vxpsykbwcpfbna4prxqvqk89n0y9jn9s44l1";
   };
 
   nativeBuildInputs = [ makeWrapper ];

pkgs/development/tools/coursier/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "coursier-${version}";
-  version = "1.0.1";
+  version = "1.1.0-M10";
 
   src = fetchurl {
     url = "https://github.com/coursier/coursier/raw/v${version}/coursier";
-    sha256 = "1rn1vb33zfl9iy80fhqvi9ykdjxz029nah5yfr5xixcx9al0bai3";
+    sha256 = "14iq0717vdm0mj0196idc724vmxp1y0f3gfn41sbqahfhvcx05y8";
   };
 
   nativeBuildInputs = [ makeWrapper ];

pkgs/development/tools/pyre/default.nix

@@ -3,12 +3,12 @@
 let
   # Manually set version - the setup script requires
   # hg and git + keeping the .git directory around.
-  pyre-version = "0.0.18";  # also change typeshed revision below with $pyre-src/.typeshed-version
+  pyre-version = "0.0.20";  # also change typeshed revision below with $pyre-src/.typeshed-version
   pyre-src = fetchFromGitHub {
     owner = "facebook";
     repo = "pyre-check";
     rev = "v${pyre-version}";
-    sha256 = "1sy1lk9j3hq20dabfkr9s4r7prrcndrs345a5iqz6yzvakr4r74d";
+    sha256 = "1alkhdhvmigdhxvvarh0lr5s3b1s6q4arykip2dqb62vs8064s17";
   };
   versionFile = writeScript "version.ml" ''
     cat > "./version.ml" <<EOF
@@ -83,8 +83,8 @@ typeshed = stdenv.mkDerivation {
   src = fetchFromGitHub {
     owner = "python";
     repo = "typeshed";
-    rev = "bc3f9fe1d3c43b00c04cedb23e0eeebc9e1734b6";
+    rev = "0b49ce75b478fdf283dda5dd1368759ac342dfe2";
-    sha256 = "06b2kj4n49h4sgi8hn5kalmir8llhanfdc7f1924cxvrkj5ry94b";
+    sha256 = "1w5aqbbcfk5ki8n9fgdikkyadjb318ipqyi517s9xnwlzi1jv0fh";
   };
   phases = [ "unpackPhase" "installPhase" ];
   installPhase = "cp -r $src $out";

pkgs/servers/nosql/neo4j/default.nix

@@ -4,21 +4,22 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "neo4j-${version}";
-  version = "3.4.10";
+  version = "3.5.2";
 
   src = fetchurl {
     url = "https://neo4j.com/artifact.php?name=neo4j-community-${version}-unix.tar.gz";
-    sha256 = "0wxcwsnnwk08w3zaz67aa93ysrl61lsy41xynq1sy6z31a7gx9jr";
+    sha256 = "0i36vgs6b24bdhckgkhw23g59x1f2zg6h07c73jv55sdmxmcdpn1";
   };
 
   buildInputs = [ makeWrapper jre8 which gawk ];
 
+
   installPhase = ''
     mkdir -p "$out/share/neo4j"
     cp -R * "$out/share/neo4j"
 
     mkdir -p "$out/bin"
-    for NEO4J_SCRIPT in neo4j neo4j-admin neo4j-import neo4j-shell cypher-shell
+    for NEO4J_SCRIPT in neo4j neo4j-admin neo4j-import cypher-shell
     do
         makeWrapper "$out/share/neo4j/bin/$NEO4J_SCRIPT" \
             "$out/bin/$NEO4J_SCRIPT" \

pkgs/servers/sip/freeswitch/default.nix

@@ -1,7 +1,10 @@
-{ fetchurl, stdenv, ncurses, curl, pkgconfig, gnutls, readline
+{ fetchurl, stdenv, lib, ncurses, curl, pkgconfig, gnutls, readline
 , openssl, perl, sqlite, libjpeg, speex, pcre
 , ldns, libedit, yasm, which, lua, libopus, libsndfile
 
+, postgresql
+, enablePostgres ? true
+
 , SystemConfiguration
 }:
 
@@ -23,12 +26,16 @@ stdenv.mkDerivation rec {
     openssl ncurses curl gnutls readline perl libjpeg
     sqlite pcre speex ldns libedit yasm which lua libopus
     libsndfile
-  ] ++ stdenv.lib.optionals stdenv.isDarwin [ SystemConfiguration ];
+  ]
+  ++ lib.optionals enablePostgres [ postgresql ]
+  ++ lib.optionals stdenv.isDarwin [ SystemConfiguration ];
 
   NIX_CFLAGS_COMPILE = "-Wno-error";
 
   hardeningDisable = [ "format" ];
 
+  configureFlags = lib.optionals enablePostgres [ "--enable-core-pgsql-support" ];
+
   meta = {
     description = "Cross-Platform Scalable FREE Multi-Protocol Soft Switch";
     homepage = https://freeswitch.org/;

pkgs/servers/sql/postgresql/ext/pg_topn.nix

@@ -1,17 +1,16 @@
-{ stdenv, fetchFromGitHub, postgresql, protobufc }:
+{ stdenv, fetchFromGitHub, postgresql }:
 
 stdenv.mkDerivation rec {
   name = "pg_topn-${version}";
-  version = "2.2.0";
+  version = "2.2.2";
 
-  nativeBuildInputs = [ protobufc ];
   buildInputs = [ postgresql ];
 
   src = fetchFromGitHub {
     owner  = "citusdata";
     repo   = "postgresql-topn";
     rev    = "refs/tags/v${version}";
-    sha256 = "1i5fn517mdvzfhlcj7fh4z0iniynanshcn7kzhsq19sgci0g31fr";
+    sha256 = "1bh28nrxj06vc2cvlsxlwrwad5ff3lfj3kr5cnnggwjk2dhwbbjm";
   };
 
   installPhase = ''
@@ -24,7 +23,7 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Efficient querying of 'top values' for PostgreSQL";
-    homepage    = https://www.citusdata.com/;
+    homepage    = https://github.com/citusdata/postgresql-topn;
     maintainers = with maintainers; [ thoughtpolice ];
     platforms   = platforms.linux;
     license     = licenses.agpl3;

pkgs/tools/graphics/oxipng/default.nix

@@ -1,17 +1,20 @@
 { stdenv, fetchFromGitHub, rustPlatform }:
 
 rustPlatform.buildRustPackage rec {
-  version = "2.1.8";
+  version = "2.2.0";
   name = "oxipng-${version}";
 
   src = fetchFromGitHub {
     owner = "shssoichiro";
     repo = "oxipng";
     rev = "v${version}";
-    sha256 = "18ld65vm58s6x918g6bhfkrg7lw2lca8daidv88ff14wm5khjvik";
+    sha256 = "00ys1dy8r1g84j04w50qcjas0qnfw4vphazvbfasd9q2b1p5z69l";
   };
 
-  cargoSha256 = "034i8hgi0zgv085bimlja1hl3nd096rqpi167pw6rda5aj18c625";
+  cargoSha256 = "125r3jmgwcq8qddm8hjpyzaam96kkifaxixksyaw2iqk9xq0nrpm";
+
+  # https://crates.io/crates/cloudflare-zlib#arm-vs-nightly-rust
+  cargoBuildFlags = [ "--features=cloudflare-zlib/arm-always" ];
 
   meta = with stdenv.lib; {
     homepage = https://github.com/shssoichiro/oxipng;
@@ -19,8 +22,5 @@ rustPlatform.buildRustPackage rec {
     license = licenses.mit;
     maintainers = with maintainers; [ dywedir ];
     platforms = platforms.all;
-
-    # Needs newer/unstable rust: error[E0658]: macro is_arm_feature_detected! is unstable
-    broken = stdenv.isAarch64;
   };
 }

pkgs/tools/graphics/pfstools/default.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchurl, cmake, pkgconfig
 , openexr, zlib, imagemagick, libGLU_combined, freeglut, fftwFloat
-, fftw, gsl, libexif, perl, opencv, qt4
+, fftw, gsl, libexif, perl, opencv, qt5
 }:
 
 stdenv.mkDerivation rec {
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake pkgconfig ];
   buildInputs = [
     openexr zlib imagemagick libGLU_combined freeglut fftwFloat
-    fftw gsl libexif perl opencv qt4
+    fftw gsl libexif perl opencv qt5.qtbase
   ];
 
   patches = [ ./threads.patch ./pfstools.patch ];

pkgs/tools/misc/moreutils/default.nix

@@ -23,7 +23,10 @@ stdenv.mkDerivation rec {
   buildFlags = "CC=cc";
   installFlags = "PREFIX=$(out)";
 
-  postInstall = "wrapProgram $out/bin/chronic --prefix PERL5LIB : $PERL5LIB";
+  postInstall = ''
+    wrapProgram $out/bin/chronic --prefix PERL5LIB : $PERL5LIB
+    wrapProgram $out/bin/ts --prefix PERL5LIB : $PERL5LIB
+  '';
 
   meta = {
     description = "Growing collection of the unix tools that nobody thought to write long ago when unix was young";

pkgs/tools/misc/ostree/default.nix

@@ -1,34 +1,17 @@
-{ stdenv, fetchFromGitHub, fetchpatch, pkgconfig, gtk-doc, gobject-introspection, gnome3
+{ stdenv, fetchurl, fetchpatch, pkgconfig, gtk-doc, gobject-introspection, gnome3
 , glib, systemd, xz, e2fsprogs, libsoup, gpgme, which, autoconf, automake, libtool, fuse, utillinuxMinimal, libselinux
 , libarchive, libcap, bzip2, yacc, libxslt, docbook_xsl, docbook_xml_dtd_42, python3
 }:
 
-let
+stdenv.mkDerivation rec {
-  version = "2018.9";
+  pname = "ostree";
-
+  version = "2019.1";
-  libglnx-src = fetchFromGitHub {
-    owner = "GNOME";
-    repo = "libglnx";
-    rev = "470af8763ff7b99bec950a6ae0a957c1dcfc8edd";
-    sha256 = "1fwik38i6w3r6pn4qkizradcqp1m83n7ljh9jg0y3p3kvrbfxh15";
-  };
-
-  bsdiff-src = fetchFromGitHub {
-    owner = "mendsley";
-    repo = "bsdiff";
-    rev = "1edf9f656850c0c64dae260960fabd8249ea9c60";
-    sha256 = "1h71d2h2d3anp4msvpaff445rnzdxii3id2yglqk7af9i43kdsn1";
-  };
-in stdenv.mkDerivation {
-  name = "ostree-${version}";
 
   outputs = [ "out" "dev" "man" "installedTests" ];
 
-  src = fetchFromGitHub {
+  src = fetchurl {
-    rev = "v${version}";
+    url = "https://github.com/ostreedev/ostree/releases/download/v${version}/libostree-${version}.tar.xz";
-    owner = "ostreedev";
+    sha256 = "08y7nsxl305dnlfak4kyj88lld848y4kg6bvjqngcxaqqvkk9xqm";
-    repo = "ostree";
-    sha256 = "0a8gr4qqxcvz3fqv9w4dxy6iq0rq4kdzf08rzv8xg4gic3ldgyvj";
   };
 
   patches = [
@@ -57,13 +40,6 @@ in stdenv.mkDerivation {
     (python3.withPackages (p: with p; [ pyyaml ])) gnome3.gjs # for tests
   ];
 
-  prePatch = ''
-    rmdir libglnx bsdiff
-    cp --no-preserve=mode -r ${libglnx-src} libglnx
-    cp --no-preserve=mode -r ${bsdiff-src} bsdiff
-  '';
-
-
   preConfigure = ''
     env NOCONFIGURE=1 ./autogen.sh
   '';
@@ -71,17 +47,16 @@ in stdenv.mkDerivation {
   enableParallelBuilding = true;
 
   configureFlags = [
-    "--with-systemdsystemunitdir=$(out)/lib/systemd/system"
+    "--with-systemdsystemunitdir=${placeholder "out"}/lib/systemd/system"
-    "--with-systemdsystemgeneratordir=$(out)/lib/systemd/system-generators"
+    "--with-systemdsystemgeneratordir=${placeholder "out"}/lib/systemd/system-generators"
     "--enable-installed-tests"
   ];
 
   makeFlags = [
-    "installed_testdir=$(installedTests)/libexec/installed-tests/libostree"
+    "installed_testdir=${placeholder "installedTests"}/libexec/installed-tests/libostree"
-    "installed_test_metadir=$(installedTests)/share/installed-tests/libostree"
+    "installed_test_metadir=${placeholder "installedTests"}/share/installed-tests/libostree"
   ];
 
-
   meta = with stdenv.lib; {
     description = "Git for operating system binaries";
     homepage = https://ostree.readthedocs.io/en/latest/;

pkgs/tools/misc/papis/default.nix

@@ -1,52 +1,52 @@
-{ lib, fetchFromGitHub, bashInteractive
+{ lib, fetchFromGitHub, fetchpatch
-, python3, vim
+, python36, xdg_utils
 }:
 
-let
+python36.pkgs.buildPythonApplication rec {
-  python = python3;
-
-in python.pkgs.buildPythonApplication rec {
   pname = "papis";
-  version = "0.6";
+  version = "0.7.5";
 
   # Missing tests on Pypi
   src = fetchFromGitHub {
     owner = "papis";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0zy8q154zhpqb75c775nwq3mdl1szhzhkfi0nvyjmzfgsv2g1wa2";
+    sha256 = "1b481sj92z9nw7gwbrpkgd4nlmqc1n73qilkc51k2r56cy1kjvss";
   };
 
-  postPatch = ''
+  # Update click version to 7.0.0
-    sed -i 's/configparser>=3.0.0/# configparser>=3.0.0/' setup.py
+  patches = fetchpatch {
-    patchShebangs tests
+    url = https://github.com/papis/papis/commit/fddb80978a37a229300b604c26e992e2dc90913f.patch;
-  '';
+    sha256 = "0cmagfdaaml1pxhnxggifpb47z5g1p231qywnvnqpd3dm93382w1";
+  };
 
-  propagatedBuildInputs = with python.pkgs; [
+  propagatedBuildInputs = with python36.pkgs; [
-    argcomplete arxiv2bib beautifulsoup4 bibtexparser
+    click requests filetype pyparsing configparser
-    configparser dmenu-python habanero papis-python-rofi
+    arxiv2bib pyyaml chardet beautifulsoup4 prompt_toolkit
-    pylibgen prompt_toolkit pyparser python_magic pyyaml
+    bibtexparser python-slugify pyparser pylibgen
-    requests unidecode urwid vobject tkinter whoosh
+    habanero isbnlib
-    vim
+    # optional dependencies
+    dmenu-python whoosh
   ];
 
-  checkInputs = with python.pkgs; [ pytest ];
+  postInstall = ''
-
+    install -Dt "$out/etc/bash_completion.d" scripts/shell_completion/build/bash/papis
-  # Papis tries to create the config folder under $HOME during the tests
-  checkPhase = ''
-    mkdir -p check-phase
-    export PATH=$out/bin:$PATH
-    # Still don't know why this fails
-    sed -i 's/--set dir=hello //' tests/bash/test_default.sh
-
-    # This test has been disabled since it requires a network connaction
-    sed -i 's/test_downloader_getter(self):/disabled_test_downloader_getter(self):/' papis/downloaders/tests/test_main.py
-
-    export HOME=$(pwd)/check-phase
-    make test
-    SH=${bashInteractive}/bin/bash make test-non-pythonic
   '';
 
+  checkInputs = (with python36.pkgs; [
+    pytest
+  ]) ++ [
+    xdg_utils
+  ];
+
+  # most of the downloader tests require a network connection
+  checkPhase = ''
+    HOME=$(mktemp -d) pytest papis tests --ignore tests/downloaders
+  '';
+
+  # FIXME: find out why 39 tests fail
+  doCheck = false;
+
   meta = {
     description = "Powerful command-line document and bibliography manager";
     homepage = http://papis.readthedocs.io/en/latest/;

pkgs/tools/misc/rpm-ostree/default.nix

@@ -1,39 +1,28 @@
-{ stdenv, fetchpatch, fetchFromGitHub, ostree, rpm, which, autoconf, automake, libtool, pkgconfig,
+{ stdenv, fetchurl, ostree, rpm, which, autoconf, automake, libtool, pkgconfig, cargo, rustc,
-  gobject-introspection, gtk-doc, libxml2, libxslt, docbook_xsl, docbook_xml_dtd_42, gperf, cmake,
+  gobject-introspection, gtk-doc, libxml2, libxslt, docbook_xsl, docbook_xml_dtd_42, docbook_xml_dtd_43, gperf, cmake,
   libcap, glib, systemd, json-glib, libarchive, libsolv, librepo, polkit,
   bubblewrap, pcre, check, python }:
 
-let
+stdenv.mkDerivation rec {
-  libglnx-src = fetchFromGitHub {
+  pname = "rpm-ostree";
-    owner = "GNOME";
+  version = "2019.1";
-    repo = "libglnx";
+
-    rev = "97b5c08d2f93dc93ba296a84bbd2a5ab9bd8fc97";
+  src = fetchurl {
-    sha256 = "0cz4x63f6ys7dln54g6mrr7hksvqwz78wdc8qb7zr1h2cp1azcvs";
+    url = "https://github.com/projectatomic/${pname}/releases/download/v${version}/${pname}-${version}.tar.xz";
+    sha256 = "14qk8mq5yc67j3wl3fa9xnhh8ii8x5qdiavf7ybw7mp4ma4lwa8k";
   };
 
-  libdnf-src = fetchFromGitHub {
+  patches = [
-    owner = "rpm-software-management";
+    # gobject-introspection requires curl in cflags
-    repo = "libdnf";
+    # https://github.com/NixOS/nixpkgs/pull/50953#issuecomment-449777169
-    rev = "b3fcc53f6f3baf4f51f836f5e1eb54eb82d5df49";
+    # https://github.com/NixOS/nixpkgs/pull/50953#issuecomment-452177080
-    sha256 = "15nl9x4blyc9922rvz7iq56yy8hxhpsf31cs3ag7aypqpfx3czci";
+    ./fix-introspection-build.patch
-  };
+  ];
-
-  version = "2018.5";
-in stdenv.mkDerivation {
-  name = "rpm-ostree-${version}";
 
   outputs = [ "out" "dev" "man" "devdoc" ];
-
-  src = fetchFromGitHub {
-    rev = "v${version}";
-    owner = "projectatomic";
-    repo = "rpm-ostree";
-    sha256 = "0y37hr8mmrsww4ka2hlqmz7wp57ibzhah4j87yg8q8dks5hxcbsx";
-  };
-
   nativeBuildInputs = [
-    pkgconfig which autoconf automake libtool cmake gperf
+    pkgconfig which autoconf automake libtool cmake gperf cargo rustc
-    gobject-introspection gtk-doc libxml2 libxslt docbook_xsl docbook_xml_dtd_42
+    gobject-introspection gtk-doc libxml2 libxslt docbook_xsl docbook_xml_dtd_42 docbook_xml_dtd_43
   ];
   buildInputs = [
     libcap ostree rpm glib systemd polkit bubblewrap
@@ -41,14 +30,6 @@ in stdenv.mkDerivation {
     pcre check python
   ];
 
-  patches = [
-    # Use gdbus-codegen from PATH
-    (fetchpatch {
-      url = https://github.com/projectatomic/rpm-ostree/commit/315406d8cd0937e786723986e88d376c88806c60.patch;
-      sha256 = "073yfa62515kyf58s0sz56w0a40062lh761y2y4assqipybwxbvp";
-    })
-  ];
-
   configureFlags = [
     "--enable-gtk-doc"
     "--with-bubblewrap=${bubblewrap}/bin/bwrap"
@@ -57,16 +38,9 @@ in stdenv.mkDerivation {
   dontUseCmakeConfigure = true;
 
   prePatch = ''
-    rmdir libglnx libdnf
-    cp --no-preserve=mode -r ${libglnx-src} libglnx
-    cp --no-preserve=mode -r ${libdnf-src} libdnf
-
     # According to #cmake on freenode, libdnf should bundle the FindLibSolv.cmake module
     cp ${libsolv}/share/cmake/Modules/FindLibSolv.cmake libdnf/cmake/modules/
 
-    # libdnf normally wants sphinx to build its hawkey manpages, but we don't care about those manpages since we don't use hawkey
-    substituteInPlace configure.ac --replace 'cmake \' 'cmake -DWITH_MAN=off \'
-
     # Let's not hardcode the rpm-gpg path...
     substituteInPlace libdnf/libdnf/dnf-keyring.cpp \
       --replace '"/etc/pki/rpm-gpg"' 'getenv("LIBDNF_RPM_GPG_PATH_OVERRIDE") ? getenv("LIBDNF_RPM_GPG_PATH_OVERRIDE") : "/etc/pki/rpm-gpg"'
@@ -84,4 +58,3 @@ in stdenv.mkDerivation {
     platforms = platforms.linux;
   };
 }
-

pkgs/tools/misc/rpm-ostree/fix-introspection-build.patch

@@ -0,0 +1,11 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -103,7 +103,7 @@
+ 				     ostree-1 >= 2018.9
+ 				     libsystemd
+ 				     polkit-gobject-1
+-				     rpm librepo libsolv
++				     rpm librepo libsolv libcurl
+ 				     libarchive])
+ 
+ dnl -ldl: https://github.com/ostreedev/ostree/commit/1f832597fc83fda6cb8daf48c4495a9e1590774c

pkgs/tools/networking/urlwatch/default.nix

@@ -2,17 +2,18 @@
 
 python3Packages.buildPythonApplication rec {
   name = "urlwatch-${version}";
-  version = "2.15";
+  version = "2.16";
 
   src = fetchFromGitHub {
     owner  = "thp";
     repo   = "urlwatch";
     rev    = version;
-    sha256 = "1bkd0r5arzdvinpn1n23cw1gf7byxml95hl6qvvf6mnggb1ifcwg";
+    sha256 = "1bkwr151bnv72aka2r9jwaq8lkz1p6031wr5pss4sij978qn5xld";
   };
 
   propagatedBuildInputs = with python3Packages; [
     appdirs
+    cssselect
     keyring
     lxml
     minidb

pkgs/top-level/all-packages.nix

@@ -2728,7 +2728,9 @@ in
   frostwire = callPackage ../applications/networking/p2p/frostwire { };
   frostwire-bin = callPackage ../applications/networking/p2p/frostwire/frostwire-bin.nix { };
 
-  ftgl = callPackage ../development/libraries/ftgl { };
+  ftgl = callPackage ../development/libraries/ftgl {
+    inherit (darwin.apple_sdk.frameworks) OpenGL;
+  };
 
   ftop = callPackage ../os-specific/linux/ftop { };
 
@@ -15729,7 +15731,7 @@ in
 
   papirus-icon-theme = callPackage ../data/icons/papirus-icon-theme { };
 
-  papis = python3Packages.callPackage ../tools/misc/papis { };
+  papis = callPackage ../tools/misc/papis { };
 
   pecita = callPackage ../data/fonts/pecita {};
 

pkgs/top-level/haskell-packages.nix

@@ -9,8 +9,8 @@ let
     "ghc863Binary"
     "ghc844"
     "ghcjs"
-    "ghcjs82"
     "ghcjs84"
+    "ghcjs86"
     "integer-simple"
   ];
 
@@ -83,18 +83,19 @@ in {
       buildLlvmPackages = buildPackages.llvmPackages_6;
       llvmPackages = pkgs.llvmPackages_6;
     };
-    ghcjs = compiler.ghcjs84;
+    ghcjs = compiler.ghcjs86;
-    ghcjs82 = callPackage ../development/compilers/ghcjs-ng {
-      bootPkgs = packages.ghc822;
-      ghcjsSrcJson = ../development/compilers/ghcjs-ng/8.2/git.json;
-      stage0 = ../development/compilers/ghcjs-ng/8.2/stage0.nix;
-    };
     ghcjs84 = callPackage ../development/compilers/ghcjs-ng {
       bootPkgs = packages.ghc844;
       ghcjsSrcJson = ../development/compilers/ghcjs-ng/8.4/git.json;
       stage0 = ../development/compilers/ghcjs-ng/8.4/stage0.nix;
       ghcjsDepOverrides = callPackage ../development/compilers/ghcjs-ng/8.4/dep-overrides.nix {};
     };
+    ghcjs86 = callPackage ../development/compilers/ghcjs-ng {
+      bootPkgs = packages.ghc863;
+      ghcjsSrcJson = ../development/compilers/ghcjs-ng/8.6/git.json;
+      stage0 = ../development/compilers/ghcjs-ng/8.6/stage0.nix;
+      ghcjsDepOverrides = callPackage ../development/compilers/ghcjs-ng/8.6/dep-overrides.nix {};
+    };
 
     # The integer-simple attribute set contains all the GHC compilers
     # build with integer-simple instead of integer-gmp.
@@ -155,31 +156,19 @@ in {
       ghc = bh.compiler.ghcHEAD;
       compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-head.nix { };
     };
-    ghcjs = packages.ghcjs84;
+    ghcjs = packages.ghcjs86;
-    ghcjs710 = callPackage ../development/haskell-modules rec {
-      buildHaskellPackages = ghc.bootPkgs;
-      ghc = bh.compiler.ghcjs710;
-      compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-7.10.x.nix { };
-      packageSetConfig = callPackage ../development/haskell-modules/configuration-ghcjs.nix { };
-    };
-    ghcjs80 = callPackage ../development/haskell-modules rec {
-      buildHaskellPackages = ghc.bootPkgs;
-      ghc = bh.compiler.ghcjs80;
-      compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-8.0.x.nix { };
-      packageSetConfig = callPackage ../development/haskell-modules/configuration-ghcjs.nix { };
-    };
-    ghcjs82 = callPackage ../development/haskell-modules rec {
-      buildHaskellPackages = ghc.bootPkgs;
-      ghc = bh.compiler.ghcjs82;
-      compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-8.2.x.nix { };
-      packageSetConfig = callPackage ../development/haskell-modules/configuration-ghcjs.nix { };
-    };
     ghcjs84 = callPackage ../development/haskell-modules rec {
       buildHaskellPackages = ghc.bootPkgs;
       ghc = bh.compiler.ghcjs84;
       compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-8.4.x.nix { };
       packageSetConfig = callPackage ../development/haskell-modules/configuration-ghcjs.nix { };
     };
+    ghcjs86 = callPackage ../development/haskell-modules rec {
+      buildHaskellPackages = ghc.bootPkgs;
+      ghc = bh.compiler.ghcjs86;
+      compilerConfig = callPackage ../development/haskell-modules/configuration-ghc-8.6.x.nix { };
+      packageSetConfig = callPackage ../development/haskell-modules/configuration-ghcjs.nix { };
+    };
 
     # The integer-simple attribute set contains package sets for all the GHC compilers
     # using integer-simple instead of integer-gmp.

pkgs/top-level/python-packages.nix

@@ -1766,6 +1766,8 @@ in {
 
   fb-re2 = callPackage ../development/python-modules/fb-re2 { };
 
+  filetype = callPackage ../development/python-modules/filetype { };
+
   flexmock = callPackage ../development/python-modules/flexmock { };
 
   flit = callPackage ../development/python-modules/flit { };
@@ -1901,6 +1903,8 @@ in {
 
   ipfsapi = callPackage ../development/python-modules/ipfsapi { };
 
+  isbnlib = callPackage ../development/python-modules/isbnlib { };
+
   itsdangerous = callPackage ../development/python-modules/itsdangerous { };
 
   iniparse = callPackage ../development/python-modules/iniparse { };