Merge master into staging-next

179 files changed, 1325 insertions, 1024 deletions

diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index f61144fa68e..6cb9d07fe93 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -3396,7 +3396,11 @@
     github = "kmein";
     githubId = 10352507;
   };
-
+  knairda = {
+    email = "adrian@kummerlaender.eu";
+    name = "Adrian Kummerlaender";
+    github = "KnairdA";
+  };
   knedlsepp = {
     email = "josef.kemetmueller@gmail.com";
     github = "knedlsepp";
diff --git a/nixos/modules/config/sysctl.nix b/nixos/modules/config/sysctl.nix
index fb2b58eed72..e59c7a32c28 100644
--- a/nixos/modules/config/sysctl.nix
+++ b/nixos/modules/config/sysctl.nix
@@ -54,7 +54,7 @@ in
 
     # Hide kernel pointers (e.g. in /proc/modules) for unprivileged
     # users as these make it easier to exploit kernel vulnerabilities.
-    boot.kernel.sysctl."kernel.kptr_restrict" = 1;
+    boot.kernel.sysctl."kernel.kptr_restrict" = mkDefault 1;
 
     # Disable YAMA by default to allow easy debugging.
     boot.kernel.sysctl."kernel.yama.ptrace_scope" = mkDefault 0;
diff --git a/nixos/modules/installer/cd-dvd/installation-cd-graphical-kde.nix b/nixos/modules/installer/cd-dvd/installation-cd-graphical-kde.nix
index 559899b0a3b..1dc7920ff64 100644
--- a/nixos/modules/installer/cd-dvd/installation-cd-graphical-kde.nix
+++ b/nixos/modules/installer/cd-dvd/installation-cd-graphical-kde.nix
@@ -22,14 +22,8 @@ with lib;
 
   system.activationScripts.installerDesktop = let
 
-    manualDesktopFile = pkgs.writeScript "nixos-manual.desktop" ''
-      [Desktop Entry]
-      Version=1.0
-      Type=Application
-      Name=NixOS Manual
-      Exec=firefox ${config.system.build.manual.manual}/share/doc/nixos/index.html
-      Icon=text-html
-    '';
+    # Comes from documentation.nix when xserver and nixos.enable are true.
+    manualDesktopFile = "/run/current-system/sw/share/applications/nixos-manual.desktop";
 
     homeDir = "/home/nixos/";
     desktopDir = homeDir + "Desktop/";
diff --git a/nixos/modules/installer/cd-dvd/iso-image.nix b/nixos/modules/installer/cd-dvd/iso-image.nix
index d5c92cfc1d9..93c8ebaa249 100644
--- a/nixos/modules/installer/cd-dvd/iso-image.nix
+++ b/nixos/modules/installer/cd-dvd/iso-image.nix
@@ -165,8 +165,8 @@ let
     else
       "# No refind for ${targetArch}"
   ;
-  
-  grubPkgs = if config.boot.loader.grub.forcei686 then pkgs.pkgsi686Linux else pkgs; 
+
+  grubPkgs = if config.boot.loader.grub.forcei686 then pkgs.pkgsi686Linux else pkgs;
 
   grubMenuCfg = ''
     #
@@ -562,8 +562,6 @@ in
 
     boot.initrd.availableKernelModules = [ "squashfs" "iso9660" "uas" ];
 
-    boot.blacklistedKernelModules = [ "nouveau" ];
-
     boot.initrd.kernelModules = [ "loop" ];
 
     # Closures to be copied to the Nix store on the CD, namely the init
diff --git a/nixos/modules/services/monitoring/prometheus/exporters/wireguard.nix b/nixos/modules/services/monitoring/prometheus/exporters/wireguard.nix
index 8ae2c927b58..82e881236ad 100644
--- a/nixos/modules/services/monitoring/prometheus/exporters/wireguard.nix
+++ b/nixos/modules/services/monitoring/prometheus/exporters/wireguard.nix
@@ -42,6 +42,14 @@ in {
         Whether or not the remote IP of a WireGuard peer should be exposed via prometheus.
       '';
     };
+
+    addr = mkOption {
+      type = types.str;
+      default = "0.0.0.0";
+      description = ''
+        IP address of the exporter.
+      '';
+    };
   };
   serviceOpts = {
     path = [ pkgs.wireguard-tools ];
@@ -51,6 +59,7 @@ in {
       ExecStart = ''
         ${pkgs.prometheus-wireguard-exporter}/bin/prometheus_wireguard_exporter \
           -p ${toString cfg.port} \
+          -l ${cfg.addr} \
           ${optionalString cfg.verbose "-v"} \
           ${optionalString cfg.singleSubnetPerField "-s"} \
           ${optionalString cfg.withRemoteIp "-r"} \
diff --git a/nixos/modules/services/x11/display-managers/gdm.nix b/nixos/modules/services/x11/display-managers/gdm.nix
index 0a5d52e319e..6c785396613 100644
--- a/nixos/modules/services/x11/display-managers/gdm.nix
+++ b/nixos/modules/services/x11/display-managers/gdm.nix
@@ -42,10 +42,7 @@ in
     services.xserver.displayManager.gdm = {
 
       enable = mkEnableOption ''
-        GDM as the display manager.
-        <emphasis>GDM in NixOS is not well-tested with desktops other
-        than GNOME, so use with caution, as it could render the
-        system unusable.</emphasis>
+        GDM, the GNOME Display Manager
       '';
 
       debug = mkEnableOption ''
diff --git a/nixos/modules/tasks/filesystems/zfs.nix b/nixos/modules/tasks/filesystems/zfs.nix
index 2ed8c5aa292..cfdc0a31020 100644
--- a/nixos/modules/tasks/filesystems/zfs.nix
+++ b/nixos/modules/tasks/filesystems/zfs.nix
@@ -268,7 +268,12 @@ in
     };
 
     services.zfs.trim = {
-      enable = mkEnableOption "Enables periodic TRIM on all ZFS pools.";
+      enable = mkOption {
+        description = "Whether to enable periodic TRIM on all ZFS pools.";
+        default = true;
+        example = false;
+        type = types.bool;
+      };
 
       interval = mkOption {
         default = "weekly";
diff --git a/nixos/modules/tasks/network-interfaces.nix b/nixos/modules/tasks/network-interfaces.nix
index 7351f8b6b7e..29310f6f24a 100644
--- a/nixos/modules/tasks/network-interfaces.nix
+++ b/nixos/modules/tasks/network-interfaces.nix
@@ -1092,7 +1092,7 @@ in
         destination = "/etc/udev/rules.d/98-${name}";
         text = ''
           # enable and prefer IPv6 privacy addresses by default
-          ACTION=="add", SUBSYSTEM=="net", RUN+="${pkgs.coreutils}/bin/echo 2 > /proc/sys/net/ipv6/conf/%k/use_tempaddr"
+          ACTION=="add", SUBSYSTEM=="net", RUN+="${pkgs.bash}/bin/sh -c 'echo 2 > /proc/sys/net/ipv6/conf/%k/use_tempaddr'"
         '';
       })
       (pkgs.writeTextFile rec {
diff --git a/pkgs/applications/audio/linuxsampler/default.nix b/pkgs/applications/audio/linuxsampler/default.nix
index 26fc2408d8a..f13f10d15e8 100644
--- a/pkgs/applications/audio/linuxsampler/default.nix
+++ b/pkgs/applications/audio/linuxsampler/default.nix
@@ -3,11 +3,11 @@
 
 stdenv.mkDerivation rec {
   pname = "linuxsampler";
-  version = "2.1.0";
+  version = "2.1.1";
 
   src = fetchurl {
     url = "https://download.linuxsampler.org/packages/${pname}-${version}.tar.bz2";
-    sha256 = "0fdxpw7jjfi058l95131d6d8538h05z7n94l60i6mhp9xbplj2jf";
+    sha256 = "1gijf50x5xbpya5dj3v2mzj7azx4qk9p012csgddp73f0qi0n190";
   };
 
   preConfigure = ''
diff --git a/pkgs/applications/audio/lollypop/default.nix b/pkgs/applications/audio/lollypop/default.nix
index 73d8d350f38..c967576a5aa 100644
--- a/pkgs/applications/audio/lollypop/default.nix
+++ b/pkgs/applications/audio/lollypop/default.nix
@@ -71,9 +71,8 @@ python3.pkgs.buildPythonApplication rec  {
     patchShebangs meson_post_install.py
   '';
 
-  preFixup = ''
-    buildPythonPath "$out $propagatedBuildInputs"
-    patchPythonScript "$out/libexec/lollypop-sp"
+  postFixup = ''
+    wrapPythonProgramsIn $out/libexec "$out $propagatedBuildInputs"
   '';
 
   # Produce only one wrapper using wrap-python passing
diff --git a/pkgs/applications/audio/ncmpc/default.nix b/pkgs/applications/audio/ncmpc/default.nix
index d89b61aa21f..4fa9626332b 100644
--- a/pkgs/applications/audio/ncmpc/default.nix
+++ b/pkgs/applications/audio/ncmpc/default.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   pname = "ncmpc";
-  version = "0.34";
+  version = "0.35";
 
   src = fetchFromGitHub {
     owner  = "MusicPlayerDaemon";
     repo   = "ncmpc";
     rev    = "v${version}";
-    sha256 = "0ffby37qdg251c1w0vl6rmd13akbydnf12468z4vrl0ybwfd7fc4";
+    sha256 = "0hhc5snxy5fbg47ynz4b7fkmzdy974zxqr0cqc6kh15yvbr25ikh";
   };
 
   buildInputs = [ glib ncurses mpd_clientlib boost ];
diff --git a/pkgs/applications/audio/pulseaudio-ctl/default.nix b/pkgs/applications/audio/pulseaudio-ctl/default.nix
index 1ad57efda7a..6b7d242e1f6 100644
--- a/pkgs/applications/audio/pulseaudio-ctl/default.nix
+++ b/pkgs/applications/audio/pulseaudio-ctl/default.nix
@@ -7,13 +7,13 @@ let
 
 in stdenv.mkDerivation rec {
   name = "${pname}-${version}";
-  version = "1.66";
+  version = "1.67";
 
   src = fetchFromGitHub {
     owner = "graysky2";
     repo = pname;
     rev = "v${version}";
-    sha256 = "19a24w7y19551ar41q848w7r1imqkl9cpff4dpb7yry7qp1yjg0y";
+    sha256 = "1mf5r7x6aiqmx9mz7gpckrqvvzxnr5gs2q1k4m42rjk6ldkpdb46";
   };
 
   postPatch = ''
diff --git a/pkgs/applications/audio/pulseeffects/default.nix b/pkgs/applications/audio/pulseeffects/default.nix
index 83fb17189e1..2a68f9a64f2 100644
--- a/pkgs/applications/audio/pulseeffects/default.nix
+++ b/pkgs/applications/audio/pulseeffects/default.nix
@@ -47,13 +47,13 @@ let
   ];
 in stdenv.mkDerivation rec {
   pname = "pulseeffects";
-  version = "4.6.6";
+  version = "4.6.8";
 
   src = fetchFromGitHub {
     owner = "wwmm";
     repo = "pulseeffects";
     rev = "v${version}";
-    sha256 = "15w1kc1b0i8wrkrbfzrvcscanxvcsz336bfyi1awb1lbclvd3sf4";
+    sha256 = "09crsg73mvqdknvh6lczwx16x73zb2vb3m53bsapqiaq4lmwy3qr";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/audio/qmmp/default.nix b/pkgs/applications/audio/qmmp/default.nix
index ef52c65b105..aee373329ce 100644
--- a/pkgs/applications/audio/qmmp/default.nix
+++ b/pkgs/applications/audio/qmmp/default.nix
@@ -29,11 +29,11 @@
 # handle that.
 
 mkDerivation rec {
-  name = "qmmp-1.3.3";
+  name = "qmmp-1.3.4";
 
   src = fetchurl {
     url = "http://qmmp.ylsoftware.com/files/${name}.tar.bz2";
-    sha256 = "1777kqgvbkshqlawy00gbgwflxflwmjjidqdq29mhqszs76r6727";
+    sha256 = "0j9vgm6216w7arwl919p9rps0a9r6s4415spl3qkpifhwlk90zg0";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
diff --git a/pkgs/applications/blockchains/ledger-live-desktop/default.nix b/pkgs/applications/blockchains/ledger-live-desktop/default.nix
index 0417d2913de..88b35dd78a6 100644
--- a/pkgs/applications/blockchains/ledger-live-desktop/default.nix
+++ b/pkgs/applications/blockchains/ledger-live-desktop/default.nix
@@ -1,50 +1,34 @@
-{ stdenv, fetchurl, makeDesktopItem, makeWrapper, appimage-run }:
+{ stdenv, fetchurl, makeDesktopItem, appimageTools }:
 
-stdenv.mkDerivation rec {
+let
   pname = "ledger-live-desktop";
-  version = "1.12.0";
+  version = "1.15.0";
+  name = "${pname}-${version}";
 
   src = fetchurl {
     url = "https://github.com/LedgerHQ/${pname}/releases/download/v${version}/${pname}-${version}-linux-x86_64.AppImage";
-    sha256 = "0sn0ri8kqvy36d6vjwsb0mh54nwic58416m6q5drl1schsn6wyvj";
+    sha256 = "0r7gm7q7gj39v36jd5xz20931za94nf2fpf3clbghkhlbrm0kbnq";
   };
 
-  nativeBuildInputs = [ makeWrapper ];
-  buildInputs = [ appimage-run ];
-
-  desktopIcon = fetchurl {
-    url = "https://raw.githubusercontent.com/LedgerHQ/${pname}/v${version}/build/icon.png";
-    sha256 = "1mmfaf0yk7xf1kgbs3ka8wsbz1qgh60xj6z91ica1i7lw2qbdd5h";
-  };
-
-  desktopItem = makeDesktopItem {
-    name = pname;
-    exec = "${placeholder "out"}/bin/${pname}";
-    icon = pname;
-    desktopName = "Ledger Live";
-    categories = "Utility;";
+  appimageContents = appimageTools.extractType2 {
+    inherit name src;
   };
-
-  unpackPhase = ":";
-
-  installPhase = ''
-    runHook preInstall
-
-    ${desktopItem.buildCommand}
-    install -D $src $out/share/${src.name}
-    install -Dm -x ${desktopIcon} \
-      $out/share/icons/hicolor/1024x1024/apps/${pname}.png
-    makeWrapper ${appimage-run}/bin/appimage-run $out/bin/${pname} \
-      --add-flags $out/share/${src.name}
-
-    runHook postInstall
+in appimageTools.wrapType2 rec {
+  inherit name src;
+
+  extraInstallCommands = ''
+    mv $out/bin/${name} $out/bin/${pname}
+    install -m 444 -D ${appimageContents}/ledger-live-desktop.desktop $out/share/applications/ledger-live-desktop.desktop
+    install -m 444 -D ${appimageContents}/ledger-live-desktop.png $out/share/icons/hicolor/1024x1024/apps/ledger-live-desktop.png
+    substituteInPlace $out/share/applications/ledger-live-desktop.desktop \
+      --replace 'Exec=AppRun' 'Exec=${pname}'
   '';
 
   meta = with stdenv.lib; {
     description = "Wallet app for Ledger Nano S and Ledger Blue";
     homepage = "https://www.ledger.com/live";
     license = licenses.mit;
-    maintainers = with maintainers; [ thedavidmeister ];
+    maintainers = with maintainers; [ thedavidmeister nyanloutre ];
     platforms = [ "x86_64-linux" ];
   };
 }
diff --git a/pkgs/applications/blockchains/parity/beta.nix b/pkgs/applications/blockchains/parity/beta.nix
index a6d4660dff1..a26a1b7cc77 100644
--- a/pkgs/applications/blockchains/parity/beta.nix
+++ b/pkgs/applications/blockchains/parity/beta.nix
@@ -1,6 +1,6 @@
 let
-  version     = "2.6.2";
-  sha256      = "1j4249m5k3bi7di0wq6fm64zv3nlpgmg4hr5hnn94fyc09nz9n1r";
-  cargoSha256 = "1wr0i54zc3l6n0x6cvlq9zfy3bw9w5fcvdz4vmyym9r1nkvk31s7";
+  version     = "2.6.4";
+  sha256      = "11l93w97961zig4gqf345j9l20g0mjp7fayl1mdwdp14hhd5zk5g";
+  cargoSha256 = "1q6cbms7j1h726bvq38npxkjkmz14b5ir9c4z7pb0jcy7gkplyxx";
 in
   import ./parity.nix { inherit version sha256 cargoSha256; }
diff --git a/pkgs/applications/blockchains/parity/default.nix b/pkgs/applications/blockchains/parity/default.nix
index 88d24a87e13..299bb0639b6 100644
--- a/pkgs/applications/blockchains/parity/default.nix
+++ b/pkgs/applications/blockchains/parity/default.nix
@@ -1,6 +1,6 @@
 let
-  version     = "2.5.7";
-  sha256      = "0aprs71cbf98dsvjz0kydngkvdg5x7dijji8j6xadgvsarl1ljnj";
-  cargoSha256 = "11mr5q5aynli9xm4wnxcypl3ij7f4b0p7l557yi9n0cvdraw8ki4";
+  version     = "2.5.9";
+  sha256      = "06gmfw5l8n5i35dimsmj6dn0fxhbp53zjrdvbkff63r5kfqnwnx2";
+  cargoSha256 = "1kdy0bnmyqx4rhpq0a8gliy6mws68n035kfkxrfa6cxr2cn53dyb";
 in
   import ./parity.nix { inherit version sha256 cargoSha256; }
diff --git a/pkgs/applications/editors/jetbrains/default.nix b/pkgs/applications/editors/jetbrains/default.nix
index ebdfb09936a..16d5609934d 100644
--- a/pkgs/applications/editors/jetbrains/default.nix
+++ b/pkgs/applications/editors/jetbrains/default.nix
@@ -240,7 +240,7 @@ let
       patchPhase = (attrs.patchPhase or "") + optionalString (stdenv.isLinux) ''
         # Webstorm tries to use bundled jre if available.
         # Lets prevent this for the moment
-        rm -r jre64
+        rm -r jbr
       '';
     });
 in
@@ -250,12 +250,12 @@ in
 
   clion = buildClion rec {
     name = "clion-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.3"; /* updated by script */
     description  = "C/C++ IDE. New. Intelligent. Cross-platform";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/cpp/CLion-${version}.tar.gz";
-      sha256 = "13y2c3vzlklwz9cd7anpfdc3dqwh714xivm1g59s6p4x9sy172lp"; /* updated by script */
+      sha256 = "0kiqbcx64rlz1pajbn326zwy0d1vxdxpvk5xpqkcj7nva611pdq1"; /* updated by script */
     };
     wmClass = "jetbrains-clion";
     update-channel = "CLion RELEASE"; # channel's id as in http://www.jetbrains.com/updates/updates.xml
@@ -263,12 +263,12 @@ in
 
   datagrip = buildDataGrip rec {
     name = "datagrip-${version}";
-    version = "2019.2.2"; /* updated by script */
+    version = "2019.2.5"; /* updated by script */
     description = "Your Swiss Army Knife for Databases and SQL";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/datagrip/${name}.tar.gz";
-      sha256 = "1babydzmgaas1rxjv11yhgbp0l5scsdwy17l9927qwlbgccf24mb"; /* updated by script */
+      sha256 = "18frmlchalpvc55j25ig2slf2h33gwmbmm8dvc29jb3kgsl0ny7p"; /* updated by script */
     };
     wmClass = "jetbrains-datagrip";
     update-channel = "DataGrip RELEASE";
@@ -276,12 +276,12 @@ in
 
   goland = buildGoland rec {
     name = "goland-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.2"; /* updated by script */
     description = "Up and Coming Go IDE";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/go/${name}.tar.gz";
-      sha256 = "16wmsf6c8x95d050grqgv6aaxlkc6pqhbqzlz6fzsngjnbkn64yj"; /* updated by script */
+      sha256 = "1wq1prgfn6wc7lc6qjhiykm62c56yrb5rv0hyylcsgdw0q3ns6z2"; /* updated by script */
     };
     wmClass = "jetbrains-goland";
     update-channel = "GoLand RELEASE";
@@ -289,12 +289,12 @@ in
 
   idea-community = buildIdea rec {
     name = "idea-community-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.3"; /* updated by script */
     description = "Integrated Development Environment (IDE) by Jetbrains, community edition";
     license = stdenv.lib.licenses.asl20;
     src = fetchurl {
       url = "https://download.jetbrains.com/idea/ideaIC-${version}.tar.gz";
-      sha256 = "1pbqnyqly09m7lw6356dydbvppq4i94rsk7c3y40mrc285qzj413"; /* updated by script */
+      sha256 = "0gy42x49yhdnp4ks6445xbc24dxw2vxnl12hdyx03mszdv0r58ni"; /* updated by script */
     };
     wmClass = "jetbrains-idea-ce";
     update-channel = "IntelliJ IDEA RELEASE";
@@ -302,12 +302,12 @@ in
 
   idea-ultimate = buildIdea rec {
     name = "idea-ultimate-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.3"; /* updated by script */
     description = "Integrated Development Environment (IDE) by Jetbrains, requires paid license";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/idea/ideaIU-${version}-no-jbr.tar.gz";
-      sha256 = "0mslmhakjjgwj76hbfw9dcidic6zprjfjryggic7dqywl7vjwc95"; /* updated by script */
+      sha256 = "0allnibq8van3n1c5y85gscbpls0wshwffa6b2l2andw1jkhc259"; /* updated by script */
     };
     wmClass = "jetbrains-idea";
     update-channel = "IntelliJ IDEA RELEASE";
@@ -315,12 +315,12 @@ in
 
   phpstorm = buildPhpStorm rec {
     name = "phpstorm-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.3"; /* updated by script */
     description = "Professional IDE for Web and PHP developers";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/webide/PhpStorm-${version}.tar.gz";
-      sha256 = "1m198p6586dych6mrgwqxs486qndypsmnikl0rxx45ddrwfjl42g"; /* updated by script */
+      sha256 = "0pra0hmyczxcxnvsc7rqiwhwj23ckx97c9m1wcyn7ik612xwik1i"; /* updated by script */
     };
     wmClass = "jetbrains-phpstorm";
     update-channel = "PhpStorm RELEASE";
@@ -328,12 +328,12 @@ in
 
   pycharm-community = buildPycharm rec {
     name = "pycharm-community-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.3"; /* updated by script */
     description = "PyCharm Community Edition";
     license = stdenv.lib.licenses.asl20;
     src = fetchurl {
       url = "https://download.jetbrains.com/python/${name}.tar.gz";
-      sha256 = "0a3fi2wjj0166199pyhvvpaih9nx0xr6q7zf7jfj8i7khpkdk8i5"; /* updated by script */
+      sha256 = "02fynwi54libibgigwggh6xaf5p4046n0kjsqsck1kjbnrlghp10"; /* updated by script */
     };
     wmClass = "jetbrains-pycharm-ce";
     update-channel = "PyCharm RELEASE";
@@ -341,12 +341,12 @@ in
 
   pycharm-professional = buildPycharm rec {
     name = "pycharm-professional-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.3"; /* updated by script */
     description = "PyCharm Professional Edition";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/python/${name}.tar.gz";
-      sha256 = "03i7qi0kcnx0irih468xaz7hzicaa5yh399r676drs22ak23qwrq"; /* updated by script */
+      sha256 = "19i3ll8p69n7jw7psv2nkhjq899gljwmc5ixpqhyl203rykavb7n"; /* updated by script */
     };
     wmClass = "jetbrains-pycharm";
     update-channel = "PyCharm RELEASE";
@@ -354,12 +354,12 @@ in
 
   rider = buildRider rec {
     name = "rider-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.2"; /* updated by script */
     description = "A cross-platform .NET IDE based on the IntelliJ platform and ReSharper";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/rider/JetBrains.Rider-${version}.tar.gz";
-      sha256 = "1p0mlch7qvkvgxjscx6rl65v6h8g6fwk8rcb8s27qkcjm0d78ic8"; /* updated by script */
+      sha256 = "1wv5vhiv3w1dwyklx1pr5javp4psqyiv4naq37cvxxp9zh7hk8rc"; /* updated by script */
     };
     wmClass = "jetbrains-rider";
     update-channel = "Rider RELEASE";
@@ -367,12 +367,12 @@ in
 
   ruby-mine = buildRubyMine rec {
     name = "ruby-mine-${version}";
-    version = "2019.2.1"; /* updated by script */
+    version = "2019.2.3"; /* updated by script */
     description = "The Most Intelligent Ruby and Rails IDE";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/ruby/RubyMine-${version}.tar.gz";
-      sha256 = "0l0kwc1mih55px8j6bvp1g3pxrv0scd9vpydwvkaqmq5x0r1n3jf"; /* updated by script */
+      sha256 = "0g8yxsq9xn8l8wnmcm0y5y0ll5081s83mmwrb62k4bldlsr25iba"; /* updated by script */
     };
     wmClass = "jetbrains-rubymine";
     update-channel = "RubyMine RELEASE";
@@ -380,12 +380,12 @@ in
 
   webstorm = buildWebStorm rec {
     name = "webstorm-${version}";
-    version = "2019.1.3"; /* updated by script */
+    version = "2019.2.3"; /* updated by script */
     description = "Professional IDE for Web and JavaScript development";
     license = stdenv.lib.licenses.unfree;
     src = fetchurl {
       url = "https://download.jetbrains.com/webstorm/WebStorm-${version}.tar.gz";
-      sha256 = "1bhx2p40r15zvfr6q10bj5y8jaa3i9x9adchczp0irkd3w2jgvy3"; /* updated by script */
+      sha256 = "0l3c3b1d53b3w90d4g99pjw8vmjj716jjaxsv4hy53shh1ncd55g"; /* updated by script */
     };
     wmClass = "jetbrains-webstorm";
     update-channel = "WebStorm RELEASE";
diff --git a/pkgs/applications/kde/default.nix b/pkgs/applications/kde/default.nix
index 9b146aa5036..70a716a760c 100644
--- a/pkgs/applications/kde/default.nix
+++ b/pkgs/applications/kde/default.nix
@@ -172,6 +172,7 @@ let
       pim-data-exporter = callPackage ./pim-data-exporter.nix {};
       pim-sieve-editor = callPackage ./pim-sieve-editor.nix {};
       print-manager = callPackage ./print-manager.nix {};
+      rocs = callPackage ./rocs.nix {};
       spectacle = callPackage ./spectacle.nix {};
       yakuake = callPackage ./yakuake.nix {};
       # Okteta was removed from kde applications and will now be released independently
diff --git a/pkgs/applications/kde/pim-data-exporter.nix b/pkgs/applications/kde/pim-data-exporter.nix
index d17ffb3c044..9f2117b41fb 100644
--- a/pkgs/applications/kde/pim-data-exporter.nix
+++ b/pkgs/applications/kde/pim-data-exporter.nix
@@ -1,10 +1,10 @@
 {
   mkDerivation, lib, kdepimTeam,
   extra-cmake-modules, kdoctools,
-  akonadi, kcmutils, kcrash, kdbusaddons, kidentitymanagement, kldap,
-  kmailtransport, knewstuff, knotifications, knotifyconfig, kparts, kross, ktexteditor,
-  kwallet, libkdepim, libkleo, pimcommon, qttools,
-  karchive, mailcommon, messagelib
+  akonadi, akonadi-notes, kcalcore, kcmutils, kcrash, kdbusaddons,
+  kidentitymanagement, kldap, kmailtransport, knewstuff, knotifications,
+  knotifyconfig, kparts, kross, ktexteditor, kwallet, libkdepim, libkleo,
+  pimcommon, qttools, karchive, mailcommon, messagelib
 }:
 
 mkDerivation {
@@ -15,8 +15,9 @@ mkDerivation {
   };
   nativeBuildInputs = [ extra-cmake-modules kdoctools ];
   buildInputs = [
-    akonadi kcmutils kcrash kdbusaddons kidentitymanagement kldap kmailtransport
-    knewstuff knotifications knotifyconfig kparts kross ktexteditor kwallet libkdepim
-    libkleo pimcommon qttools karchive mailcommon messagelib
+    akonadi akonadi-notes kcalcore kcmutils kcrash kdbusaddons
+    kidentitymanagement kldap kmailtransport knewstuff knotifications
+    knotifyconfig kparts kross ktexteditor kwallet libkdepim libkleo pimcommon
+    qttools karchive mailcommon messagelib
   ];
 }
diff --git a/pkgs/applications/kde/rocs.nix b/pkgs/applications/kde/rocs.nix
new file mode 100644
index 00000000000..feae7ca81de
--- /dev/null
+++ b/pkgs/applications/kde/rocs.nix
@@ -0,0 +1,25 @@
+{
+  mkDerivation, lib,
+  extra-cmake-modules, boost,
+  qtbase, qtscript, qtquickcontrols, qtwebkit, qtxmlpatterns, grantlee,
+  kdoctools, karchive, kxmlgui, kcrash, kdeclarative, ktexteditor, kguiaddons
+}:
+
+mkDerivation {
+  name = "rocs";
+
+  meta = with lib; {
+    homepage = "https://edu.kde.org/rocs/";
+    description = "A graph theory IDE.";
+    license = with licenses; [ gpl2 lgpl21 fdl12 ];
+    platforms = lib.platforms.linux;
+    maintainers = with maintainers; [ knairda ];
+  };
+
+  nativeBuildInputs = [ extra-cmake-modules kdoctools ];
+  buildInputs = [
+    boost
+    qtbase qtscript qtquickcontrols qtwebkit qtxmlpatterns grantlee
+    kxmlgui kcrash kdeclarative karchive ktexteditor kguiaddons
+  ];
+}
diff --git a/pkgs/applications/misc/1password/default.nix b/pkgs/applications/misc/1password/default.nix
index edcd08f2499..5895990e80e 100644
--- a/pkgs/applications/misc/1password/default.nix
+++ b/pkgs/applications/misc/1password/default.nix
@@ -2,24 +2,24 @@
 
 stdenv.mkDerivation rec {
   pname = "1password";
-  version = "0.6.1";
+  version = "0.6.2";
   src =
     if stdenv.hostPlatform.system == "i686-linux" then
       fetchzip {
         url = "https://cache.agilebits.com/dist/1P/op/pkg/v${version}/op_linux_386_v${version}.zip";
-        sha256 = "1yr78yawscp9fgvdw0dimc68k3bblk3g67g3jrqpa7hnl6pr24yl";
+        sha256 = "08ha4qr064jyivsp8z3q2cwmmm6klqyicc1i9vpf7zd9xmmx72rd";
         stripRoot = false;
       }
     else if stdenv.hostPlatform.system == "x86_64-linux" then
       fetchzip {
         url = "https://cache.agilebits.com/dist/1P/op/pkg/v${version}/op_linux_amd64_v${version}.zip";
-        sha256 = "03m0vxhghzf4zq7k2f1afkc5ixf0qwiiypqjfjgpqpfng7g9ang7";
+        sha256 = "1fjhn1k9h6rlrgin5czvpig8h70dh14i5k20g77jvxq24bf0sn9m";
         stripRoot = false;
       }
     else if stdenv.hostPlatform.system == "x86_64-darwin" then
       fetchzip {
         url = "https://cache.agilebits.com/dist/1P/op/pkg/v${version}/op_darwin_amd64_v${version}.zip";
-        sha256 = "1hypmls1fq4rjx9icgr0pkx3s3fhhma2q5rds314sv7f9ijl458f";
+        sha256 = "1x7pj41a4wra3ws09cyc063ai5isf12qbkm2hxiiiq5glnacpvpl";
         stripRoot = false;
       }
     else throw "Architecture not supported";
@@ -37,7 +37,7 @@ stdenv.mkDerivation rec {
     description  = "1Password command-line tool";
     homepage     = https://support.1password.com/command-line/;
     downloadPage = https://app-updates.agilebits.com/product_history/CLI;
-    maintainers  = with maintainers; [ joelburget ];
+    maintainers  = with maintainers; [ joelburget marsam ];
     license      = licenses.unfree;
     platforms    = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
   };
diff --git a/pkgs/applications/misc/kitty/default.nix b/pkgs/applications/misc/kitty/default.nix
index 1991cf1fa4a..db8ef004383 100644
--- a/pkgs/applications/misc/kitty/default.nix
+++ b/pkgs/applications/misc/kitty/default.nix
@@ -21,14 +21,14 @@
 with python3Packages;
 buildPythonApplication rec {
   pname = "kitty";
-  version = "0.14.5";
+  version = "0.14.6";
   format = "other";
 
   src = fetchFromGitHub {
     owner = "kovidgoyal";
     repo = "kitty";
     rev = "v${version}";
-    sha256 = "0qx3wj4n3zgjcpd1vjjwdlz8d1vp8bkxihsg2khlla1izandgxxa";
+    sha256 = "1rb5ys9xsdhd2qa3kz5gqzz111c6b14za98va6hlglk69wqlmb51";
   };
 
   buildInputs = [
@@ -89,7 +89,7 @@ buildPythonApplication rec {
     mkdir -p $out
     ${if stdenv.isDarwin then ''
     mkdir "$out/bin"
-    ln -s ../Applications/kitty.app/Contents/MacOS/kitty-deref-symlink "$out/bin/kitty"
+    ln -s ../Applications/kitty.app/Contents/MacOS/kitty "$out/bin/kitty"
     mkdir "$out/Applications"
     cp -r kitty.app "$out/Applications/kitty.app"
     '' else ''
@@ -123,6 +123,6 @@ buildPythonApplication rec {
     description = "A modern, hackable, featureful, OpenGL based terminal emulator";
     license = licenses.gpl3;
     platforms = platforms.darwin ++ platforms.linux;
-    maintainers = with maintainers; [ tex rvolosatovs ];
+    maintainers = with maintainers; [ tex rvolosatovs ma27 ];
   };
 }
diff --git a/pkgs/applications/misc/osmium-tool/default.nix b/pkgs/applications/misc/osmium-tool/default.nix
index 616949af883..19657da607f 100644
--- a/pkgs/applications/misc/osmium-tool/default.nix
+++ b/pkgs/applications/misc/osmium-tool/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "osmium-tool";
-  version = "1.10.0";
+  version = "1.11.0";
 
   src = fetchFromGitHub {
     owner = "osmcode";
     repo = "osmium-tool";
     rev = "v${version}";
-    sha256 = "1balhz78nva0agmbp8n9vg8fhmdssnd9fjxj20bpw7b45mxhjc20";
+    sha256 = "164r1w539dzy67ir2rqh21kwdvkjv87isd18gp51qyxbsprz6kq5";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/applications/misc/pwsafe/default.nix b/pkgs/applications/misc/pwsafe/default.nix
index 1ed54b05ec8..b1f4e5f9e42 100644
--- a/pkgs/applications/misc/pwsafe/default.nix
+++ b/pkgs/applications/misc/pwsafe/default.nix
@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   pname = "pwsafe";
-  version = "1.08.1";
+  version = "1.08.2";
 
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
     rev = "${version}BETA";
-    sha256 = "0x89pn056h8b4yvxbd6l3qwrghslxc7vlxnblmcmsx7xx4i041ng";
+    sha256 = "14qwk3cv5psj7ll71ikyv452x55c7iwjw9765yrpij6741r4yjln";
   };
 
   nativeBuildInputs = [ 
diff --git a/pkgs/applications/misc/sequeler/default.nix b/pkgs/applications/misc/sequeler/default.nix
index e3edb539928..78c9fed17fe 100644
--- a/pkgs/applications/misc/sequeler/default.nix
+++ b/pkgs/applications/misc/sequeler/default.nix
@@ -11,13 +11,13 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "sequeler";
-  version = "0.7.2";
+  version = "0.7.3";
 
   src = fetchFromGitHub {
     owner = "Alecaddd";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0mxlhyfqmd4zg0psdmr62rhmvssw8jslm7a1nvh93675ns3vfrs5";
+    sha256 = "16vc3v9qls9fxg9h8fsi67z68s4acl5hj14gbcrnqm7mf3kmk3aw";
   };
 
   nativeBuildInputs = [ meson ninja pkgconfig pantheon.vala gettext wrapGAppsHook python3 desktop-file-utils ];
diff --git a/pkgs/applications/misc/syncthingtray/default.nix b/pkgs/applications/misc/syncthingtray/default.nix
index 0dc8f3bf38e..70aa684da04 100644
--- a/pkgs/applications/misc/syncthingtray/default.nix
+++ b/pkgs/applications/misc/syncthingtray/default.nix
@@ -20,14 +20,14 @@
 }:
 
 mkDerivation rec {
-  version = "0.9.1";
+  version = "0.10.0";
   pname = "syncthingtray";
 
   src = fetchFromGitHub {
     owner = "Martchus";
     repo = "syncthingtray";
     rev = "v${version}";
-    sha256 = "0ijwpwlwwbfh9fdfbwz6dgi6hpmaav2jm56mzxm6as50iwnb59fx";
+    sha256 = "18h6z6baaiyr0wr7kyz6ysg45zb12550m63j3vqiap4hfrrwhly5";
   };
 
   buildInputs = [ qtbase cpp-utilities qtutilities ]
diff --git a/pkgs/applications/networking/browsers/eolie/default.nix b/pkgs/applications/networking/browsers/eolie/default.nix
index e067f3f15eb..b9b183a03ff 100644
--- a/pkgs/applications/networking/browsers/eolie/default.nix
+++ b/pkgs/applications/networking/browsers/eolie/default.nix
@@ -5,7 +5,7 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "eolie";
-  version = "0.9.60";
+  version = "0.9.63";
 
   format = "other";
   doCheck = false;
@@ -14,7 +14,7 @@ python3.pkgs.buildPythonApplication rec {
     url = "https://gitlab.gnome.org/World/eolie";
     rev = "refs/tags/${version}";
     fetchSubmodules = true;
-    sha256 = "1mhl7p8pwp8lqx5z15r0lx1y4mb2c1gjwy3w6041cyc4hyb91693";
+    sha256 = "0z8gcfg7i842rr5p8r3vqa31kf7nnj1yv3afax3jzf4zbnhb8wm0";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/networking/instant-messengers/pybitmessage/default.nix b/pkgs/applications/networking/instant-messengers/pybitmessage/default.nix
index 3f6b23d70a0..111f4e728e7 100644
--- a/pkgs/applications/networking/instant-messengers/pybitmessage/default.nix
+++ b/pkgs/applications/networking/instant-messengers/pybitmessage/default.nix
@@ -12,14 +12,15 @@ python2Packages.buildPythonApplication rec {
     sha256 = "1lmhbpwsqh1v93krlqqhafw2pc3y0qp8zby186yllbph6s8kdp35";
   };
 
-  propagatedBuildInputs = with python2Packages; [ msgpack-python pyqt4 numpy pyopencl ] ++ [ openssl ];
+  propagatedBuildInputs = with python2Packages; [ msgpack pyqt4 numpy pyopencl setuptools ] ++ [ openssl ];
 
   preConfigure = ''
     # Remove interaction and misleading output
     substituteInPlace setup.py \
       --replace "nothing = raw_input()" pass \
       --replace 'print "It looks like building the package failed.\n" \' pass \
-      --replace '    "You may be missing a C++ compiler and the OpenSSL headers."' pass
+      --replace '    "You may be missing a C++ compiler and the OpenSSL headers."' pass \
+      --replace 'msgpack-python' 'msgpack'
 
     substituteInPlace src/pyelliptic/openssl.py \
       --replace "libdir.append(find_library('ssl'))" "libdir.append('${openssl.out}/lib/libssl.so')"
diff --git a/pkgs/applications/networking/instant-messengers/riot/riot-desktop-package.json b/pkgs/applications/networking/instant-messengers/riot/riot-desktop-package.json
index b9017c12d60..cfc38fb4ae7 100644
--- a/pkgs/applications/networking/instant-messengers/riot/riot-desktop-package.json
+++ b/pkgs/applications/networking/instant-messengers/riot/riot-desktop-package.json
@@ -2,7 +2,7 @@
   "name": "riot-web",
   "productName": "Riot",
   "main": "src/electron-main.js",
-  "version": "1.3.5",
+  "version": "1.4.0",
   "description": "A feature-rich client for Matrix.org",
   "author": "New Vector Ltd.",
   "dependencies": {
diff --git a/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix b/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix
index 1fde990e4a8..885e90a98c4 100644
--- a/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix
+++ b/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix
@@ -6,12 +6,12 @@
 
 let
   executableName = "riot-desktop";
-  version = "1.3.5";
+  version = "1.4.0";
   riot-web-src = fetchFromGitHub {
     owner = "vector-im";
     repo = "riot-web";
     rev = "v${version}";
-    sha256 = "05xwp6062lvjsy539swa6dxj3k3dw1667nkx8ffwdl1dg17wphy8";
+    sha256 = "1p8bl7v2214shywn53fpcb27vvvdjrs3kcys3f045v2l5fg5xhsa";
   };
 
 in yarn2nix-moretea.mkYarnPackage rec {
diff --git a/pkgs/applications/networking/instant-messengers/riot/riot-web.nix b/pkgs/applications/networking/instant-messengers/riot/riot-web.nix
index b938f4f47cf..d0ee71b9969 100644
--- a/pkgs/applications/networking/instant-messengers/riot/riot-web.nix
+++ b/pkgs/applications/networking/instant-messengers/riot/riot-web.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   pname = "riot-web";
-  version = "1.3.5";
+  version = "1.4.0";
 
   src = fetchurl {
     url = "https://github.com/vector-im/riot-web/releases/download/v${version}/riot-v${version}.tar.gz";
-    sha256 = "0vpfv5rvrhrws52j4lxnj1qyagf9894znpxkdnkp72g19qsjn66g";
+    sha256 = "1si11hxkfn6sqaq1hddm5vkfrd0pghzwqld1wv4vxlb5jyn32qqk";
   };
 
   installPhase = let
diff --git a/pkgs/applications/networking/instant-messengers/teamspeak/client.nix b/pkgs/applications/networking/instant-messengers/teamspeak/client.nix
index eaf9a8f47e5..a75d0c8633a 100644
--- a/pkgs/applications/networking/instant-messengers/teamspeak/client.nix
+++ b/pkgs/applications/networking/instant-messengers/teamspeak/client.nix
@@ -33,13 +33,13 @@ in
 stdenv.mkDerivation rec {
   pname = "teamspeak-client";
 
-  version = "3.3.0";
+  version = "3.3.2";
 
   src = fetchurl {
     url = "https://files.teamspeak-services.com/releases/client/${version}/TeamSpeak3-Client-linux_${arch}-${version}.run";
     sha256 = if stdenv.is64bit
-                then "13286dbjp4qiyfv8my1hfpwzns4szdsnqa11j8ygsh5ikgjk338a"
-                else "04lwclq7nvw73v5fmn9795j5wi54syglc77ldl41caiqqhdqf1i5";
+                then "1n916ds67dxj5bfgc5zm9nz2xh2914k85pzzspzvfyr7njcw7hpi"
+                else "0csl5xklcb4v8bzwvby5m2n38zjrnaw8dcvha7qvfbjllxr75yn2";
   };
 
   # grab the plugin sdk for the desktop icon
diff --git a/pkgs/applications/networking/mailreaders/thunderbird-bin/release_sources.nix b/pkgs/applications/networking/mailreaders/thunderbird-bin/release_sources.nix
index 2de09fc73f4..6dfb6780f0d 100644
--- a/pkgs/applications/networking/mailreaders/thunderbird-bin/release_sources.nix
+++ b/pkgs/applications/networking/mailreaders/thunderbird-bin/release_sources.nix
@@ -1,615 +1,615 @@
 {
-  version = "68.1.0";
+  version = "68.1.1";
   sources = [
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-x86_64/ar/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-x86_64/ar/thunderbird-68.1.1.tar.bz2";
       locale = "ar";
       arch = "linux-x86_64";
-      sha512 = "b9bb22bdbe013358c03e804e3c51ad387dca503b9e0074db70494eb3f331d72bd8679db929972e75b39f2464d384753bcab9947d1a843a69167d7b3706952c35";
+      sha512 = "33accd6fe1f83fc47a34df038f4257571f42281a89f9aab2f54514443856b71aaa2ee81abe98331ecdbbf026a09eea31fb2c5eb72044347c54f51a6ac1e0bfd4";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-x86_64/ast/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-x86_64/ast/thunderbird-68.1.1.tar.bz2";
       locale = "ast";
       arch = "linux-x86_64";
-      sha512 = "e00382241343bbd8a86e31dfcf5bbb060b46e5db6211cfa54c7192361353e2c4fe3d0ad3f4e0319ec1a0dc1f4590b7bc0271e5658bc468986d8e27a64d9924da";
+      sha512 = "1e32c40cd198b51a5836c2ad9a6331c0b3028e57d62e5e057990a48ab80b9fd5bd1290a268da29dc5a45c61e712bf0345f85d0ca43c18b2236c0f4bac7b9328f";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-x86_64/be/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-x86_64/be/thunderbird-68.1.1.tar.bz2";
       locale = "be";
       arch = "linux-x86_64";
-      sha512 = "f043c8aa5dac0d5e2f9da628d6659f654cc39726677424e4b5e5005e97bf202575f569ebdee346d37cc8d4d59da188e6cfe1bd6bf7df1acafe26b489242b4a9f";
+      sha512 = "0f86506a7cf72c75712f6b507fda6e39da9520865dea5eb4fbfdb78531dc88116d4e8227dd91e8f1fb4dff9ed3e4eb7e118b5a4dde3860ec00c3bca625478a21";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-x86_64/bg/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-x86_64/bg/thunderbird-68.1.1.tar.bz2";
       locale = "bg";
       arch = "linux-x86_64";
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       arch = "linux-i686";
-      sha512 = "f602557748517324943b5ff276f4efdeca1c5083662bc9f0b0bdba8c10510cee834b3883870a98d51d406f58e338a09d0589b3bc0891bfbd88b895cca02fd360";
+      sha512 = "6345bfa3abf1ec899320696b10553f0a75b48f2f2dc317c5d6ac10ddaf09a7269353a73aec84ef4d7501d064e409d434054711441da3698f1ed5af653de4970f";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/sk/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/sk/thunderbird-68.1.1.tar.bz2";
       locale = "sk";
       arch = "linux-i686";
-      sha512 = "7b6980d2b5131bd9a43a29efa2f1e97c60e15410a63224d839548d777fd8b4c4d65ccfc7756227cf900f7420b12231c3d48f062133cb6f21bbdcdcdb179f2e47";
+      sha512 = "745514c55e85f71cf07bda02a842c8452c454a80a10bfea20e9c5750f1702809b4c589a2c1d3127c599a91ac0fab458de8c4d66afc8511e64278f02638fff63c";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/sl/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/sl/thunderbird-68.1.1.tar.bz2";
       locale = "sl";
       arch = "linux-i686";
-      sha512 = "ecc38fb4fde66b7b213b1cfeb8ab170b3e685d0a28c7e071e19a85509ec74e79fb6eb61104c47f0eef1a77e1e1a52b292469a364747eeccc701c522452c58351";
+      sha512 = "2449333ceec017fd3b6e3bf673c3aa553b9c52c07a09e02e773e42e2c6acec60573183d6a09c5c085ed9389c1d48c4f02acf50d83499421bedb3094823ddb34d";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/sq/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/sq/thunderbird-68.1.1.tar.bz2";
       locale = "sq";
       arch = "linux-i686";
-      sha512 = "3ff668c6ed28bdb2f3d388ab8ecb1bf3b2b38bb29046b8559f7b9f9c6fa32db226c4620f472ba5a982b473e3e3f4aee04aa3746e57738b512dcb37fdfd5ecfc5";
+      sha512 = "7a2ac8f6c04cbdbc222ea1218dcc64928b6d5038381a7655db34cd568717854197fe4b77645b2ea07b4b76a724c2e8196db693c5e367d09367edf1af471f358e";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/sr/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/sr/thunderbird-68.1.1.tar.bz2";
       locale = "sr";
       arch = "linux-i686";
-      sha512 = "4c71511375333802f903cb632963933054a969c02a3fb23f4416e0cb3c21e18147bbffb28572f8ac90aa5bc3c4138b25590c42610c20a14b5e8eddb1edf28c28";
+      sha512 = "06db22ff1ed32c1311d62d1cb860bb22686d5893985bf16fe2effaff864b4352788889d5e2f2ff6c450edd4be9d9c1f33ddcff513d5eb2cc3e88fe5e50c33485";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/sv-SE/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/sv-SE/thunderbird-68.1.1.tar.bz2";
       locale = "sv-SE";
       arch = "linux-i686";
-      sha512 = "5d7d569f4eb9ed738f54139a90e9a01e9e771a553af193357d45765bd54815a096ddc31ac69620d6f14516e8f41f1c0fb8f16a848e13273d0c18b9c047d85fb4";
+      sha512 = "f1a43a44dc155a01cda07041f554eb3474c35621ee8d8c7596aeee2746da12aa934d94f436014218a360b7848888d0e49285ca66cca8209b7b02d044c29571f4";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/tr/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/tr/thunderbird-68.1.1.tar.bz2";
       locale = "tr";
       arch = "linux-i686";
-      sha512 = "fc8892f85032d9fcce76c3fa971531f4039b8bb9e1812776bb3e7c5b68474543b5db4007f79e81abc1685c74f0574201236aab8a2df05ac10fcaade7c57ca3c2";
+      sha512 = "e430c26852fd2cc3b9afabe9f8c3e1480e3454614bd90c766dce2b2cf652fe526146f79bdc0e25a1ce4979c1e22c0af90540659df5fdae89b0498428a61e0d1b";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/uk/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/uk/thunderbird-68.1.1.tar.bz2";
       locale = "uk";
       arch = "linux-i686";
-      sha512 = "80335f326bde31f4b1e269cd756b4b41ff3a632023f09447abf6d1964381f8f9657a4f47ed6af63a3eb0cd4e84e5bced595eec07cc0a9e30ad8d3cf3d08026df";
+      sha512 = "d6717aee4e1367ba031d03a90fc46ef397f9bbe6ef1d2a5537df77dca1d042e83c6fb44baef9ab01dc47de0f481742186220542831bfb6670c7a756a77eddfad";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/uz/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/uz/thunderbird-68.1.1.tar.bz2";
       locale = "uz";
       arch = "linux-i686";
-      sha512 = "2434a8a063b0d1019220579bc83160217d5c269b24ad83a9ed0969425a1fc9d9ed8b190c291d87c34379928aa6c2329d3b5ad287b44177dd61f680081cd7caf9";
+      sha512 = "58ba68d642eeb1700c6d0994260bb16028fd15b49697c6e99e61e73d90275e0e4d2e6957c2af60122ca7be8804c1ddeb15dc38090287335a674104da3cd1cb47";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/vi/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/vi/thunderbird-68.1.1.tar.bz2";
       locale = "vi";
       arch = "linux-i686";
-      sha512 = "0e33f1a2f8cd67bdb523180af0b8afa5fbbb3628b0b9407f2a4ae609c7155b33fd85a1f23d9b74097fefb045fd0b437f58971cc4c4d5f391398d6ea7429b921e";
+      sha512 = "9968cf02fe2b58f21e228b9292b48fcf9df5beb805335e7c77332231690b2bfcea29a4abfe9e834a85c2e4f79fe55df4590a2ec17676712c1b30736f48704bf8";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/zh-CN/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/zh-CN/thunderbird-68.1.1.tar.bz2";
       locale = "zh-CN";
       arch = "linux-i686";
-      sha512 = "27d1d9b3c30ab1dd863362139f91b79ffb7e36e87ff1f7f07162ea3e86a58962136e43cca3212e4263908f63dfe3a3c53bb3db3085e5b4bf07e0ff88408822d8";
+      sha512 = "41369b102e82285050147d0e883fc20c6b7d311a1a8cef2efd31480a6eeee8c3ea5e0a9e9968c3d903d1fd92aeec331ade3cbcedd16cb254a74c6049ec0ab410";
     }
-    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.0/linux-i686/zh-TW/thunderbird-68.1.0.tar.bz2";
+    { url = "http://archive.mozilla.org/pub/thunderbird/releases/68.1.1/linux-i686/zh-TW/thunderbird-68.1.1.tar.bz2";
       locale = "zh-TW";
       arch = "linux-i686";
-      sha512 = "2141f0ad5d11daf3a94f3a737801ec0234a7f2d869320d4859d771ab92a6e59bf13139b4048a7239640635051a9228e6cbf55746402ed35cb398d93a3d129439";
+      sha512 = "37e07f78c2ab67d040d6cd4a511fb3e6a641ca00dd659b51d5d320e79251bb2096dd6719da819c22306e10af9fc88389212129d20064ce110d06d49bf01545b5";
     }
     ];
 }
diff --git a/pkgs/applications/networking/mailreaders/thunderbird/default.nix b/pkgs/applications/networking/mailreaders/thunderbird/default.nix
index 1617ccd7dd1..574c4895a64 100644
--- a/pkgs/applications/networking/mailreaders/thunderbird/default.nix
+++ b/pkgs/applications/networking/mailreaders/thunderbird/default.nix
@@ -25,11 +25,11 @@ let
   gcc = if stdenv.cc.isGNU then stdenv.cc.cc else stdenv.cc.cc.gcc;
 in stdenv.mkDerivation rec {
   pname = "thunderbird";
-  version = "68.1.0";
+  version = "68.1.1";
 
   src = fetchurl {
     url = "mirror://mozilla/thunderbird/releases/${version}/source/thunderbird-${version}.source.tar.xz";
-    sha512 = "06036nawpm987q33567nhz55qybbcl55h5rdhjbhck5qmyj1qi383xqac5niwyk7c0gaq4ygwc5a24pysf85crjdway2zmqyjxp2apb";
+    sha512 = "2ng5wwd7fn9247ggzlxx96scc2nalaahzvxkzvb87mp9fbfcsi3v9dh370cm42px8hrknnsp2lrfk9hqx4287zyn9pl3k9vr6a9cswl";
   };
 
   # from firefox, but without sound libraries
diff --git a/pkgs/applications/radio/qradiolink/default.nix b/pkgs/applications/radio/qradiolink/default.nix
index a00ec6c47eb..4a185667944 100644
--- a/pkgs/applications/radio/qradiolink/default.nix
+++ b/pkgs/applications/radio/qradiolink/default.nix
@@ -5,7 +5,7 @@
 } :
 
 let
-  version = "0.5.0";
+  version = "0.5.2";
 
 in stdenv.mkDerivation {
   pname = "qradiolink";
@@ -15,7 +15,7 @@ in stdenv.mkDerivation {
     owner = "kantooon";
     repo = "qradiolink";
     rev = version;
-    sha256 = "0xhg5zhjznmls5m3rhpk1qx0dipxmca12s85w15d0i7qwva2f1gi";
+    sha256 = "0djhrr96b8sr2vi6hwbzgzlp9771622dp93f0rsphsyxlwbzsrgl";
   };
 
   preBuild = ''
diff --git a/pkgs/applications/science/biology/macse/default.nix b/pkgs/applications/science/biology/macse/default.nix
new file mode 100644
index 00000000000..59938addbe8
--- /dev/null
+++ b/pkgs/applications/science/biology/macse/default.nix
@@ -0,0 +1,32 @@
+{ stdenv, fetchurl, jre, makeWrapper }:
+
+stdenv.mkDerivation rec {
+  pname = "macse";
+  version = "2.03";
+
+  src = fetchurl {
+    url = "https://bioweb.supagro.inra.fr/${pname}/releases/${pname}_v${version}.jar";
+    sha256 = "0jnjyz4f255glg37rawzdv4m6nfs7wfwc5dny7afvx4dz2sv4ssh";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  dontBuild = true;
+  unpackPhase = ":";
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out/share/java
+    cp -s $src $out/share/java/macse.jar
+    makeWrapper ${jre}/bin/java $out/bin/macse --add-flags "-jar $out/share/java/macse.jar"
+    runHook postInstall
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Multiple alignment of coding sequences";
+    homepage = "https://bioweb.supagro.inra.fr/macse/";
+    license = licenses.gpl2;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/applications/science/electronics/verilog/default.nix b/pkgs/applications/science/electronics/verilog/default.nix
index f850a1bf94d..b707db14160 100644
--- a/pkgs/applications/science/electronics/verilog/default.nix
+++ b/pkgs/applications/science/electronics/verilog/default.nix
@@ -35,6 +35,6 @@ stdenv.mkDerivation rec {
     homepage = "http://iverilog.icarus.com/";
     license = licenses.lgpl21;
     maintainers = with maintainers; [ winden ];
-    platforms = platforms.linux;
+    platforms = platforms.all;
   };
 }
diff --git a/pkgs/applications/version-management/git-and-tools/hub/default.nix b/pkgs/applications/version-management/git-and-tools/hub/default.nix
index cd38be2b977..c3d0ddfe4e3 100644
--- a/pkgs/applications/version-management/git-and-tools/hub/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/hub/default.nix
@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   pname = "hub";
-  version = "2.12.4";
+  version = "2.12.7";
 
   goPackagePath = "github.com/github/hub";
 
@@ -13,7 +13,7 @@ buildGoPackage rec {
     owner = "github";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1d4cn4pgx520psrfac92h3m7azxnpj1plrrqmxryar85f3y363bq";
+    sha256 = "028hc2cgjgqmi9kvxhck4nvq02p095bp1d8qxc6q38aynwfmmhk5";
   };
 
   nativeBuildInputs = [ groff utillinux ];
diff --git a/pkgs/applications/video/minitube/default.nix b/pkgs/applications/video/minitube/default.nix
index a9876da234f..f1f757d588f 100644
--- a/pkgs/applications/video/minitube/default.nix
+++ b/pkgs/applications/video/minitube/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchFromGitHub, wrapQtAppsHook, phonon, phonon-backend-vlc, qtbase, qmake
-, qtdeclarative, qttools
+, qtdeclarative, qttools, qtx11extras, mpv
 
 # "Free" key generated by nckx <github@tobias.gr>. I no longer have a Google
 # account. You'll need to generate (and please share :-) a new one if it breaks.
@@ -7,16 +7,17 @@
 
 stdenv.mkDerivation rec {
   pname = "minitube";
-  version = "2.9";
+  version = "3.2";
 
   src = fetchFromGitHub {
-    sha256 = "11zkmwqadlgrrghs3rxq0h0fllfnyd3g09d7gdd6vd9r1a1yz73f";
+    sha256 = "0175sgqmszakqd631bni4aqjpx68h6n49zjvg23fb1yyancnkn4c";
     rev = version;
     repo = "minitube";
     owner = "flaviotordini";
+    fetchSubmodules = true;
   };
 
-  buildInputs = [ phonon phonon-backend-vlc qtbase qtdeclarative qttools ];
+  buildInputs = [ phonon phonon-backend-vlc qtbase qtdeclarative qttools qtx11extras mpv ];
   nativeBuildInputs = [ wrapQtAppsHook qmake ];
 
   qmakeFlags = [ "DEFINES+=APP_GOOGLE_API_KEY=${withAPIKey}" ];
diff --git a/pkgs/applications/virtualization/x11docker/default.nix b/pkgs/applications/virtualization/x11docker/default.nix
index ea8a24e57a3..1d18e4d14e8 100644
--- a/pkgs/applications/virtualization/x11docker/default.nix
+++ b/pkgs/applications/virtualization/x11docker/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchFromGitHub, makeWrapper, nx-libs, xorg }:
 stdenv.mkDerivation rec {
   pname = "x11docker";
-  version = "6.0.0";
+  version = "6.2.0";
   src = fetchFromGitHub {
     owner = "mviereck";
     repo = "x11docker";
     rev = "v${version}";
-    sha256 = "1sfdxlh50hv8j3dj5bphihqdyf8s7ixm6ckrmvqgr2y3gak1y840";
+    sha256 = "19q5vrhspxpjkdhhlgya2sa2fgjg8gyd3kmnb83nlfs46p8jx4f4";
   };
   nativeBuildInputs = [ makeWrapper ];
   buildInputs = [ nx-libs xorg.xhost xorg.xinit ];
diff --git a/pkgs/data/misc/osinfo-db/default.nix b/pkgs/data/misc/osinfo-db/default.nix
index b41c4a4c5aa..8af161e8707 100644
--- a/pkgs/data/misc/osinfo-db/default.nix
+++ b/pkgs/data/misc/osinfo-db/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "osinfo-db";
-  version = "20190805";
+  version = "20190920";
 
   src = fetchurl {
     url = "https://releases.pagure.org/libosinfo/${pname}-${version}.tar.xz";
-    sha256 = "1la80kmh58nrra8aa4grv31gc7xbqbybl8q1m4yv0byb11slg93x";
+    sha256 = "12kwlqljaai4fsa08m7l28v41q6244dbracvqzcbg1cs0y9jxqy8";
   };
 
   nativeBuildInputs = [ osinfo-db-tools intltool libxml2 ];
diff --git a/pkgs/desktops/pantheon/desktop/elementary-greeter/default.nix b/pkgs/desktops/pantheon/desktop/elementary-greeter/default.nix
index 963418feec0..5241aded066 100644
--- a/pkgs/desktops/pantheon/desktop/elementary-greeter/default.nix
+++ b/pkgs/desktops/pantheon/desktop/elementary-greeter/default.nix
@@ -1,6 +1,7 @@
 { stdenv
 , fetchFromGitHub
 , linkFarm
+, substituteAll
 , elementary-greeter
 , pantheon
 , pkgconfig
@@ -86,6 +87,11 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./sysconfdir-install.patch
+    # Needed until https://github.com/elementary/greeter/issues/360 is fixed
+    (substituteAll {
+      src = ./hardcode-fallback-background.patch;
+      default_wallpaper = "${nixos-artwork.wallpapers.simple-dark-gray}/share/artwork/gnome/nix-wallpaper-simple-dark-gray.png";
+    })
   ];
 
   preFixup = ''
diff --git a/pkgs/desktops/pantheon/desktop/elementary-greeter/hardcode-fallback-background.patch b/pkgs/desktops/pantheon/desktop/elementary-greeter/hardcode-fallback-background.patch
new file mode 100644
index 00000000000..556a0fc82a1
--- /dev/null
+++ b/pkgs/desktops/pantheon/desktop/elementary-greeter/hardcode-fallback-background.patch
@@ -0,0 +1,22 @@
+diff --git a/src/Cards/BackgroundImage.vala b/src/Cards/BackgroundImage.vala
+index b57fb4d..ddfd56c 100644
+--- a/src/Cards/BackgroundImage.vala
++++ b/src/Cards/BackgroundImage.vala
+@@ -9,7 +9,7 @@ public class Greeter.BackgroundImage : Gtk.EventBox {
+ 
+     public BackgroundImage (string? path) {
+         if (path == null) {
+-            path = "/usr/share/backgrounds/elementaryos-default";
++            path = "@default_wallpaper@";
+         }
+ 
+         try {
+@@ -19,7 +19,7 @@ public class Greeter.BackgroundImage : Gtk.EventBox {
+             critical ("Fallback to default wallpaper");
+ 
+             try {
+-                full_pixbuf = new Gdk.Pixbuf.from_file ("/usr/share/backgrounds/elementaryos-default");
++                full_pixbuf = new Gdk.Pixbuf.from_file ("@default_wallpaper");
+             } catch (GLib.Error e) {
+                 critical (e.message);
+             }
diff --git a/pkgs/development/compilers/intercal/default.nix b/pkgs/development/compilers/intercal/default.nix
index 6640c4aa89a..d890dc0fdfa 100644
--- a/pkgs/development/compilers/intercal/default.nix
+++ b/pkgs/development/compilers/intercal/default.nix
@@ -7,11 +7,11 @@ with stdenv.lib;
 stdenv.mkDerivation rec {
 
   pname = "intercal";
-  version = "0.30";
+  version = "0.31";
 
   src = fetchurl {
     url = "http://catb.org/esr/intercal/${pname}-${version}.tar.gz";
-    sha256 = "058ppvvgz9r5603ia9jkknbrciypgg4hjbczrv9v1d9w3ak652xk";
+    sha256 = "1z2gpa5rbqb7jscqlf258k0b0jc7d2zkyipb5csjpj6d3sw45n4k";
   };
 
   buildInputs =
diff --git a/pkgs/development/compilers/jetbrains-jdk/default.nix b/pkgs/development/compilers/jetbrains-jdk/default.nix
index a6e3dfff4e0..276b9ae150a 100644
--- a/pkgs/development/compilers/jetbrains-jdk/default.nix
+++ b/pkgs/development/compilers/jetbrains-jdk/default.nix
@@ -7,12 +7,12 @@
 
 let drv = stdenv.mkDerivation rec {
   pname = "jetbrainsjdk";
-  version = "164";
+  version = "485.1";
 
   src = if stdenv.hostPlatform.system == "x86_64-linux" then
     fetchurl {
-      url = "https://bintray.com/jetbrains/intellij-jdk/download_file?file_path=jbrsdk-11_0_2-linux-x64-b${version}.tar.gz";
-      sha256 = "121yzgvkfx7lq0k9s8wjnhz09a564br5y7zlkxgh191sbm2i7zdi";
+      url = "https://bintray.com/jetbrains/intellij-jbr/download_file?file_path=jbrsdk-11_0_4-linux-x64-b${version}.tar.gz";
+      sha256 = "18jnn0dra9nsnyllwq0ljxzr58k2pg8d0kg10y39vnxwccic4f76";
     }
   else if stdenv.hostPlatform.system == "x86_64-darwin" then
     fetchurl {
@@ -29,8 +29,7 @@ let drv = stdenv.mkDerivation rec {
   installPhase = ''
     cd ..
 
-    mv $sourceRoot $out
-    jrePath=$out/jre
+    mv $sourceRoot/jbrsdk $out
   '';
 
   postFixup = lib.optionalString (!stdenv.isDarwin) ''
diff --git a/pkgs/development/compilers/nextpnr/default.nix b/pkgs/development/compilers/nextpnr/default.nix
index 357f26cf314..d9f6f9f65dd 100644
--- a/pkgs/development/compilers/nextpnr/default.nix
+++ b/pkgs/development/compilers/nextpnr/default.nix
@@ -14,13 +14,14 @@ let
 in
 with stdenv; mkDerivation rec {
   pname = "nextpnr";
-  version = "2019.08.31";
+  version = "2019.09.28";
 
   src = fetchFromGitHub {
     owner  = "yosyshq";
     repo   = "nextpnr";
-    rev    = "c0b7379e8672b6263152d5e340e62f22179fdc8b";
-    sha256 = "174n962xiwyzy53cn192h9rq95h951k3xy6bs43p5ya592ai5mjh";
+    rev    = "7cd1e0495122847611b17a8d1f007d97a05b288c";
+    sha256 = "13y739l92plb22g73jf35pyh3y94b2vq0i65r9c31r2rb7fw4bbl";
+    fetchSubmodules = true;
   };
 
   nativeBuildInputs
@@ -34,14 +35,13 @@ with stdenv; mkDerivation rec {
   enableParallelBuilding = true;
   cmakeFlags =
     [ "-DARCH=generic;ice40;ecp5"
+      "-DBUILD_TESTS=ON"
       "-DICEBOX_ROOT=${icestorm}/share/icebox"
       "-DTRELLIS_ROOT=${trellis}/share/trellis"
       "-DPYTRELLIS_LIBDIR=${trellis}/lib/trellis"
       "-DUSE_OPENMP=ON"
       # warning: high RAM usage
       "-DSERIALIZE_CHIPDB=OFF"
-      # use PyPy for icestorm if enabled
-      "-DPYTHON_EXECUTABLE=${icestorm.pythonInterp}"
     ]
     ++ (lib.optional (!enableGui) "-DBUILD_GUI=OFF")
     ++ (lib.optional (enableGui && stdenv.isDarwin)
@@ -52,8 +52,13 @@ with stdenv; mkDerivation rec {
   patchPhase = with builtins; ''
     substituteInPlace ./CMakeLists.txt \
       --replace 'git log -1 --format=%h' 'echo ${substring 0 11 src.rev}'
+
+    # use PyPy for icestorm if enabled
+    substituteInPlace ./ice40/family.cmake \
+      --replace ''\'''${PYTHON_EXECUTABLE}' '${icestorm.pythonInterp}'
   '';
 
+  doCheck = true;
 
   postFixup = lib.optionalString enableGui ''
     wrapQtApp $out/bin/nextpnr-generic
diff --git a/pkgs/development/compilers/ponyc/default.nix b/pkgs/development/compilers/ponyc/default.nix
index 85641c351d4..6c9c9c77e6d 100644
--- a/pkgs/development/compilers/ponyc/default.nix
+++ b/pkgs/development/compilers/ponyc/default.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation ( rec {
   pname = "ponyc";
-  version = "0.30.0";
+  version = "0.31.0";
 
   src = fetchFromGitHub {
     owner = "ponylang";
     repo = pname;
     rev = version;
-    sha256 = "1gs9x4rw4mfv499j3k1brm8gbz7pjl8dyr7v68pa2f563cbzwaq9";
+    sha256 = "0cchikwga59b3p7ip9d6kxz50w5yvk1dh1dcmbix4fwfwc3zdm75";
   };
 
   buildInputs = [ llvm makeWrapper which ];
diff --git a/pkgs/development/compilers/yosys/default.nix b/pkgs/development/compilers/yosys/default.nix
index 1535c7a7de6..79c8f67b9e0 100644
--- a/pkgs/development/compilers/yosys/default.nix
+++ b/pkgs/development/compilers/yosys/default.nix
@@ -2,20 +2,21 @@
 , pkgconfig, bison, flex
 , tcl, readline, libffi, python3
 , protobuf, zlib
+, verilog
 }:
 
 with builtins;
 
 stdenv.mkDerivation rec {
   pname = "yosys";
-  version = "2019.09.01";
+  version = "2019.09.27";
 
   srcs = [
     (fetchFromGitHub {
       owner  = "yosyshq";
       repo   = "yosys";
-      rev    = "4aa505d1b254b3fbb66af2d95b396a8f077da9d0";
-      sha256 = "16rhwmn1z2ppaq3wycgq713krq48s80a6h57vgzjzj17hgncg7hs";
+      rev    = "c372e7baf9c48d41ebdbea4486a72e8dfaaddd3d";
+      sha256 = "18cyz900haf8lkpddqn0sns0a3hc8fqndzz7gg391671hzvy820k";
       name   = "yosys";
     })
 
@@ -49,6 +50,7 @@ stdenv.mkDerivation rec {
       --replace 'LD = gcc' 'LD = $(CXX)' \
       --replace 'ABCMKARGS = CC="$(CXX)" CXX="$(CXX)"' 'ABCMKARGS =' \
       --replace 'echo UNKNOWN' 'echo ${substring 0 10 (elemAt srcs 0).rev}'
+    patchShebangs tests
   '';
 
   preBuild = ''
@@ -62,6 +64,13 @@ stdenv.mkDerivation rec {
     (cd misc && ${protobuf}/bin/protoc --cpp_out ../backends/protobuf/ ./yosys.proto)
   '';
 
+  doCheck = true;
+  checkInputs = [ verilog ];
+  # checkPhase defaults to VERBOSE=y, which gets passed down to abc,
+  # which then does $(VERBOSE)gcc, which then complains about not
+  # being able to find ygcc. Life is pain.
+  checkFlags = [ " " ];
+
   meta = {
     description = "Framework for RTL synthesis tools";
     longDescription = ''
diff --git a/pkgs/development/libraries/leatherman/default.nix b/pkgs/development/libraries/leatherman/default.nix
index a84e6b5c08d..ba5dbf130b9 100644
--- a/pkgs/development/libraries/leatherman/default.nix
+++ b/pkgs/development/libraries/leatherman/default.nix
@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   pname = "leatherman";
-  version = "1.7.1";
+  version = "1.7.2";
 
   src = fetchFromGitHub {
-    sha256 = "0m2dm1gzwj0kwyl031bif89h3n4znml3m5n97hywlbra58ni8km1";
+    sha256 = "1k70fx9i4prw0vp5680ijs1ldbwd7gmvpav7jfqvpbcm3zblkc23";
     rev = version;
     repo = "leatherman";
     owner = "puppetlabs";
diff --git a/pkgs/development/libraries/libdvbpsi/default.nix b/pkgs/development/libraries/libdvbpsi/default.nix
index aed6f05fec4..3a83d01353f 100644
--- a/pkgs/development/libraries/libdvbpsi/default.nix
+++ b/pkgs/development/libraries/libdvbpsi/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "libdvbpsi";
-  version = "1.3.2";
+  version = "1.3.3";
 
   src = fetchurl {
     url = "http://get.videolan.org/libdvbpsi/${version}/${pname}-${version}.tar.bz2";
-    sha256 = "1zn5hfv4qbahmydbwh59a3b480s3m5ss27r6ml35gqdip7r3jkmc";
+    sha256 = "04h1l3vrkrdsrvkgzcr51adk10g6hxcxvgjphyyxz718ry5rkd82";
   };
 
   meta = {
diff --git a/pkgs/development/libraries/libivykis/default.nix b/pkgs/development/libraries/libivykis/default.nix
index bd1432b8a21..17cca74c7d2 100644
--- a/pkgs/development/libraries/libivykis/default.nix
+++ b/pkgs/development/libraries/libivykis/default.nix
@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
   pname = "libivykis";
 
-  version = "0.42.3";
+  version = "0.42.4";
 
   src = fetchurl {
     url = "mirror://sourceforge/libivykis/${version}/ivykis-${version}.tar.gz";
-    sha256 = "1v0ajkm531v4zxzn2x90yb5ab81ssqv2y0fib24wbsggbkajbc69";
+    sha256 = "0abi0rc3wnncvr68hy6rmzp96x6napd7fs1mff20dr8lb0jyvy3f";
   };
 
   nativeBuildInputs = [ autoreconfHook pkgconfig ];
diff --git a/pkgs/development/libraries/libosmium/default.nix b/pkgs/development/libraries/libosmium/default.nix
index eeb8fec5f93..8005fb9dbbe 100644
--- a/pkgs/development/libraries/libosmium/default.nix
+++ b/pkgs/development/libraries/libosmium/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "libosmium";
-  version = "2.15.2";
+  version = "2.15.3";
 
   src = fetchFromGitHub {
     owner = "osmcode";
     repo = "libosmium";
     rev = "v${version}";
-    sha256 = "1fh8wl4grs1c0g9whx90kd4jva3k9b6zbb1cl3isay489gwndgss";
+    sha256 = "14xpzac93f8pqjkz1r0ckqv8h691z5p6pd06wn8ib1aryzc7ps97";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/development/libraries/libpwquality/default.nix b/pkgs/development/libraries/libpwquality/default.nix
index 60c01565e63..df3595adc01 100644
--- a/pkgs/development/libraries/libpwquality/default.nix
+++ b/pkgs/development/libraries/libpwquality/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "libpwquality";
-  version = "1.4.0";
+  version = "1.4.1";
 
   src = fetchFromGitHub {
     owner = "libpwquality";
     repo = "libpwquality";
     rev = "${pname}-${version}";
-    sha256 = "0k564hj2q13z5ag8cj6rnkzm1na7001k4chz4f736p6aqvspv0bd";
+    sha256 = "150gk1d0gq9cig3ylyns7fgihgm3qb1basncahgyh1kzxplrdqm7";
   };
 
   nativeBuildInputs = [ autoreconfHook perl ];
diff --git a/pkgs/development/libraries/librseq/default.nix b/pkgs/development/libraries/librseq/default.nix
new file mode 100644
index 00000000000..d4619ba4320
--- /dev/null
+++ b/pkgs/development/libraries/librseq/default.nix
@@ -0,0 +1,37 @@
+{ stdenv, fetchFromGitHub
+, autoreconfHook, linuxHeaders
+}:
+
+stdenv.mkDerivation rec {
+  pname = "librseq";
+  version = "0.1.0pre54_${builtins.substring 0 7 src.rev}";
+
+  src = fetchFromGitHub {
+    owner  = "compudj";
+    repo   = "librseq";
+    rev    = "152600188dd214a0b2c6a8c66380e50c6ad27154";
+    sha256 = "0mivjmgdkgrr6z2gz3k6q6wgnvyvw9xzy65f6ipvqva68sxhk0mx";
+  };
+
+  outputs = [ "out" "dev" ];
+  nativeBuildInputs = [ autoreconfHook ];
+  buildInputs = [ linuxHeaders ];
+
+  separateDebugInfo = true;
+  enableParallelBuilding = true;
+
+  # The share/ subdir only contains a doc/ with a README.md that just describes
+  # how to compile the library, which clearly isn't very useful! So just get
+  # rid of it anyway.
+  postInstall = ''
+    rm -rf $out/share
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Userspace library for the Linux Restartable Sequence API";
+    homepage    = "https://github.com/compudj/librseq";
+    license     = licenses.lgpl21;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice ];
+  };
+}
diff --git a/pkgs/development/libraries/librsync/default.nix b/pkgs/development/libraries/librsync/default.nix
index 79b05619ac5..6c958feab77 100644
--- a/pkgs/development/libraries/librsync/default.nix
+++ b/pkgs/development/libraries/librsync/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "librsync";
-  version = "2.0.2";
+  version = "2.1.0";
 
   src = fetchFromGitHub {
     owner = "librsync";
     repo = "librsync";
     rev = "v${version}";
-    sha256 = "1qnr4rk93mhggqjh2025clmlhhgnjhq983p1vbh8i1g8aiqdnapi";
+    sha256 = "03ncx7a2zd93b3jaq7b62nwn8qcwmf04jfvljnpxj5wsxl2agkp7";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/development/libraries/minixml/default.nix b/pkgs/development/libraries/minixml/default.nix
index 5bdacbba11d..73b045aa964 100644
--- a/pkgs/development/libraries/minixml/default.nix
+++ b/pkgs/development/libraries/minixml/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "mxml";
-  version = "3.0";
+  version = "3.1";
 
   src = fetchFromGitHub {
     owner = "michaelrsweet";
     repo = "mxml";
     rev = "v${version}";
-    sha256 = "0madp2v2md3xq96aham91byns6qy4byd5pbg28q827fdahfhpmq7";
+    sha256 = "1kv36fxxh7bwfydhb90zjgsrvpyzvx1p5d0ayfvd3j8gip2rjhnp";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/development/libraries/ntl/default.nix b/pkgs/development/libraries/ntl/default.nix
index e83fe2e7e7b..efb307507a3 100644
--- a/pkgs/development/libraries/ntl/default.nix
+++ b/pkgs/development/libraries/ntl/default.nix
@@ -14,11 +14,11 @@ assert withGf2x -> gf2x != null;
 
 stdenv.mkDerivation rec {
   pname = "ntl";
-  version = "11.3.2";
+  version = "11.3.4";
 
   src = fetchurl {
     url = "http://www.shoup.net/ntl/ntl-${version}.tar.gz";
-    sha256 = "17bfsvn72zjqfibnxscyf4hbk3inndh4r89jd2zg7mgqmd2k3fl4";
+    sha256 = "0fdy63x6iglp20ypqhkpjj6wqjzpxlyl2wfw2dqlgiy6l6ibm4rd";
   };
 
   buildInputs = [
diff --git a/pkgs/development/libraries/openvdb/default.nix b/pkgs/development/libraries/openvdb/default.nix
index 800acebac34..3be467fdb32 100644
--- a/pkgs/development/libraries/openvdb/default.nix
+++ b/pkgs/development/libraries/openvdb/default.nix
@@ -3,13 +3,13 @@
 stdenv.mkDerivation rec
 {
   pname = "openvdb";
-  version = "6.1.0";
+  version = "6.2.0";
 
   src = fetchFromGitHub {
     owner = "dreamworksanimation";
     repo = "openvdb";
     rev = "v${version}";
-    sha256 = "0rs50741c4m0jgc7k2fdyinvm7hhjrbg0wls6whqaghbbaf1lhpk";
+    sha256 = "0ms7jmx9nsza46bky42vyb6n6p29kfjfidqg51kccvirzi07crvq";
   };
 
   outputs = [ "out" ];
diff --git a/pkgs/development/libraries/pmdk/default.nix b/pkgs/development/libraries/pmdk/default.nix
index e945154c003..eae21639110 100644
--- a/pkgs/development/libraries/pmdk/default.nix
+++ b/pkgs/development/libraries/pmdk/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "pmdk";
-  version = "1.6";
+  version = "1.6.1";
 
   src = fetchFromGitHub {
     owner  = "pmem";
     repo   = "pmdk";
     rev    = "refs/tags/${version}";
-    sha256 = "11h9h5ifgaa5f6v9y77s5lmsj7k61qg52992s1361cmvl0ndgl9k";
+    sha256 = "0iphvm9x8ly8srn3rn50qjp7339x5gpixn77n022xxr79g8jbxy6";
   };
 
   nativeBuildInputs = [ autoconf pkgconfig ];
diff --git a/pkgs/development/libraries/poco/default.nix b/pkgs/development/libraries/poco/default.nix
index e69ed0236f4..ecd20d545d5 100644
--- a/pkgs/development/libraries/poco/default.nix
+++ b/pkgs/development/libraries/poco/default.nix
@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
   pname = "poco";
 
-  version = "1.9.2";
+  version = "1.9.4";
 
   src = fetchurl {
     url = "https://pocoproject.org/releases/${pname}-${version}/${pname}-${version}-all.tar.gz";
-    sha256 = "0jkbxw6z8l7zpr7bh2xcyzk8a5apzyz4ranhl66gxna1ay0gpzvd";
+    sha256 = "0xzxi3r4v2076kcxhj7b1achma2lqy01spshxq8sfh0jn5bz4d7b";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
diff --git a/pkgs/development/libraries/qscintilla/default.nix b/pkgs/development/libraries/qscintilla/default.nix
index 43f0e431bb1..c75f324bf26 100644
--- a/pkgs/development/libraries/qscintilla/default.nix
+++ b/pkgs/development/libraries/qscintilla/default.nix
@@ -4,22 +4,26 @@
 , fixDarwinDylibNames
 }:
 
-# Fix Xcode 8 compilation problem
-let xcodePatch =
-  fetchurl { url = "https://raw.githubusercontent.com/Homebrew/formula-patches/a651d71/qscintilla2/xcode-8.patch";
-             sha256 = "1a88309fdfd421f4458550b710a562c622d72d6e6fdd697107e4a43161d69bc9"; };
-in
-stdenv.mkDerivation rec {
-  pname = "qscintilla";
-  version = "2.9.4";
+let
+  # Fix Xcode 8 compilation problem
+  xcodePatch = fetchurl {
+    url = "https://raw.githubusercontent.com/Homebrew/formula-patches/a651d71/qscintilla2/xcode-8.patch";
+    sha256 = "1a88309fdfd421f4458550b710a562c622d72d6e6fdd697107e4a43161d69bc9";
+  };
+
+  pname = "qscintilla-qt${if withQt5 then "5" else "4"}";
+  version = "2.11.2";
 
-  name = "${pname}-${if withQt5 then "qt5" else "qt4"}-${version}";
+in stdenv.mkDerivation rec {
+  inherit pname version;
 
   src = fetchurl {
-    url = "mirror://sourceforge/pyqt/QScintilla2/QScintilla-${version}/QScintilla_gpl-${version}.zip";
-    sha256 = "04678skipydx68zf52vznsfmll2v9aahr66g50lcqbr6xsmgr1yi";
+    url = "https://www.riverbankcomputing.com/static/Downloads/QScintilla/${version}/QScintilla_gpl-${version}.tar.gz";
+    sha256 = "18glb2v07mwfz6p8qmwhzcaaczyc36x3gn9wx8ndm7q6d93xr6q2";
   };
 
+  sourceRoot = "QScintilla_gpl-${version}/Qt4Qt5";
+
   buildInputs = [ (if withQt5 then qtbase else qt4) ];
 
   propagatedBuildInputs = lib.optional (withQt5 && stdenv.isDarwin) qtmacextras;
@@ -28,24 +32,23 @@ stdenv.mkDerivation rec {
     ++ (if withQt5 then [ qmake ] else [ qmake4Hook ])
     ++ lib.optional stdenv.isDarwin fixDarwinDylibNames;
 
-
   patches = lib.optional (stdenv.isDarwin && withQt5) [ xcodePatch ];
 
   enableParallelBuilding = true;
 
-  preConfigure = ''
-    cd Qt4Qt5
-    sed -i qscintilla.pro \
-      -e "s,\$\$\\[QT_INSTALL_LIBS\\],$out/lib," \
-      -e "s,\$\$\\[QT_INSTALL_HEADERS\\],$out/include/," \
-      -e "s,\$\$\\[QT_INSTALL_TRANSLATIONS\\],$out/translations," \
-    ${if withQt5 then ''
-      -e "s,\$\$\\[QT_HOST_DATA\\]/mkspecs,$out/mkspecs," \
-      -e "s,\$\$\\[QT_INSTALL_DATA\\]/mkspecs,$out/mkspecs," \
-      -e "s,\$\$\\[QT_INSTALL_DATA\\],$out/share,"
-    '' else ''
-      -e "s,\$\$\\[QT_INSTALL_DATA\\],$out/share/qt,"
-    ''}
+  # By default qscintilla will name the library with a qt version suffix which
+  # confuses the crap out of sqlitebrowser and possibly others so we simply
+  # strip the suffix as we don't need it and the various FindQScintilla.cmake
+  # files floating around *should* look for the un-suffixed version.
+  postPatch = ''
+    substituteInPlace qscintilla.pro \
+      --replace '_qt$''${QT_MAJOR_VERSION}'   "" \
+      --replace '$$[QT_INSTALL_LIBS]'         $out/lib \
+      --replace '$$[QT_INSTALL_HEADERS]'      $out/include \
+      --replace '$$[QT_INSTALL_TRANSLATIONS]' $out/translations \
+      --replace '$$[QT_HOST_DATA]/mkspecs'    $out/mkspecs \
+      --replace '$$[QT_INSTALL_DATA]/mkspecs' $out/mkspecs \
+      --replace '$$[QT_INSTALL_DATA]'         $out/share${lib.optionalString (! withQt5) "/qt"}
   '';
 
   meta = with stdenv.lib; {
@@ -64,9 +67,10 @@ stdenv.mkDerivation rec {
       proportional fonts, bold and italics, multiple foreground and
       background colours and multiple fonts.
     '';
-    homepage = http://www.riverbankcomputing.com/software/qscintilla/intro;
+    homepage = https://www.riverbankcomputing.com/software/qscintilla/intro;
     license = with licenses; [ gpl2 gpl3 ]; # and commercial
-    platforms = platforms.unix;
     maintainers = with maintainers; [ peterhoeg ];
+    platforms = platforms.unix;
+    broken = !withQt5;
   };
 }
diff --git a/pkgs/development/libraries/rdkafka/default.nix b/pkgs/development/libraries/rdkafka/default.nix
index 165e9716a97..670d2a832ee 100644
--- a/pkgs/development/libraries/rdkafka/default.nix
+++ b/pkgs/development/libraries/rdkafka/default.nix
@@ -2,16 +2,17 @@
 
 stdenv.mkDerivation rec {
   pname = "rdkafka";
-  version = "1.0.1";
+  version = "1.2.0";
 
   src = fetchFromGitHub {
     owner = "edenhill";
     repo = "librdkafka";
     rev = "v${version}";
-    sha256 = "1jxwsizqwckjzirh9gsvlca46z4y3i47vcifs1fh8gxb2lvdfgwb";
+    sha256 = "03h4yxnbnig17zapnnyvvnh1bsp0qalvlpb4fc3bpvs7yj4d8v25";
   };
 
   nativeBuildInputs = [ pkgconfig ];
+
   buildInputs = [ zlib perl python openssl ];
 
   NIX_CFLAGS_COMPILE = "-Wno-error=strict-overflow";
@@ -20,6 +21,8 @@ stdenv.mkDerivation rec {
     patchShebangs .
   '';
 
+  enableParallelBuilding = true;
+
   meta = with stdenv.lib; {
     description = "librdkafka - Apache Kafka C/C++ client library";
     homepage = https://github.com/edenhill/librdkafka;
diff --git a/pkgs/development/libraries/srt/default.nix b/pkgs/development/libraries/srt/default.nix
index 5edb2d92b55..74cdf90a156 100644
--- a/pkgs/development/libraries/srt/default.nix
+++ b/pkgs/development/libraries/srt/default.nix
@@ -4,13 +4,13 @@
 with stdenv.lib;
 stdenv.mkDerivation rec {
   pname = "srt";
-  version = "1.3.3";
+  version = "1.4.0";
 
   src = fetchFromGitHub {
     owner = "Haivision";
     repo = "srt";
     rev = "v${version}";
-    sha256 = "1dwz7qrkdrbmsbh66rbdx36b60r8whkz0wvf47jfckzsj37d2w22";
+    sha256 = "1rmswx4x3p9pdgnd7vvl3vwgh9rynakjhv1mipy2yid5rb61ajlj";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/development/mobile/cocoapods/Gemfile-beta.lock b/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
index c75dc334ebc..5a30e40293e 100644
--- a/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
+++ b/pkgs/development/mobile/cocoapods/Gemfile-beta.lock
@@ -7,15 +7,15 @@ GEM
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    algoliasearch (1.26.1)
+    algoliasearch (1.27.1)
       httpclient (~> 2.8, >= 2.8.3)
       json (>= 1.5.1)
     atomos (0.1.3)
     claide (1.0.3)
-    cocoapods (1.8.0.beta.2)
+    cocoapods (1.8.1)
       activesupport (>= 4.0.2, < 5)
       claide (>= 1.0.2, < 2.0)
-      cocoapods-core (= 1.8.0.beta.2)
+      cocoapods-core (= 1.8.1)
       cocoapods-deintegrate (>= 1.0.3, < 2.0)
       cocoapods-downloader (>= 1.2.2, < 2.0)
       cocoapods-plugins (>= 1.0.0, < 2.0)
@@ -31,10 +31,10 @@ GEM
       nap (~> 1.0)
       ruby-macho (~> 1.4)
       xcodeproj (>= 1.11.1, < 2.0)
-    cocoapods-core (1.8.0.beta.2)
+    cocoapods-core (1.8.1)
       activesupport (>= 4.0.2, < 6)
       algoliasearch (~> 1.0)
-      concurrent-ruby (~> 1.0)
+      concurrent-ruby (~> 1.1)
       fuzzy_match (~> 2.0.4)
       nap (~> 1.0)
     cocoapods-deintegrate (1.0.4)
@@ -43,7 +43,7 @@ GEM
       nap
     cocoapods-search (1.0.0)
     cocoapods-stats (1.1.0)
-    cocoapods-trunk (1.4.0)
+    cocoapods-trunk (1.4.1)
       nap (>= 0.8, < 2.0)
       netrc (~> 0.11)
     cocoapods-try (1.1.0)
@@ -57,7 +57,7 @@ GEM
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
     json (2.2.0)
-    minitest (5.11.3)
+    minitest (5.12.0)
     molinillo (0.6.6)
     nanaimo (0.2.6)
     nap (1.1.0)
diff --git a/pkgs/development/mobile/cocoapods/Gemfile.lock b/pkgs/development/mobile/cocoapods/Gemfile.lock
index b8ce7131b9f..e2de7cb0bf1 100644
--- a/pkgs/development/mobile/cocoapods/Gemfile.lock
+++ b/pkgs/development/mobile/cocoapods/Gemfile.lock
@@ -1,24 +1,27 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    CFPropertyList (3.0.0)
+    CFPropertyList (3.0.1)
     activesupport (4.2.11.1)
       i18n (~> 0.7)
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
+    algoliasearch (1.27.1)
+      httpclient (~> 2.8, >= 2.8.3)
+      json (>= 1.5.1)
     atomos (0.1.3)
-    claide (1.0.2)
-    cocoapods (1.7.5)
+    claide (1.0.3)
+    cocoapods (1.8.1)
       activesupport (>= 4.0.2, < 5)
       claide (>= 1.0.2, < 2.0)
-      cocoapods-core (= 1.7.5)
+      cocoapods-core (= 1.8.1)
       cocoapods-deintegrate (>= 1.0.3, < 2.0)
       cocoapods-downloader (>= 1.2.2, < 2.0)
       cocoapods-plugins (>= 1.0.0, < 2.0)
       cocoapods-search (>= 1.0.0, < 2.0)
       cocoapods-stats (>= 1.0.0, < 2.0)
-      cocoapods-trunk (>= 1.3.1, < 2.0)
+      cocoapods-trunk (>= 1.4.0, < 2.0)
       cocoapods-try (>= 1.1.0, < 2.0)
       colored2 (~> 3.1)
       escape (~> 0.0.4)
@@ -27,9 +30,11 @@ GEM
       molinillo (~> 0.6.6)
       nap (~> 1.0)
       ruby-macho (~> 1.4)
-      xcodeproj (>= 1.10.0, < 2.0)
-    cocoapods-core (1.7.5)
+      xcodeproj (>= 1.11.1, < 2.0)
+    cocoapods-core (1.8.1)
       activesupport (>= 4.0.2, < 6)
+      algoliasearch (~> 1.0)
+      concurrent-ruby (~> 1.1)
       fuzzy_match (~> 2.0.4)
       nap (~> 1.0)
     cocoapods-deintegrate (1.0.4)
@@ -38,7 +43,7 @@ GEM
       nap
     cocoapods-search (1.0.0)
     cocoapods-stats (1.1.0)
-    cocoapods-trunk (1.3.1)
+    cocoapods-trunk (1.4.1)
       nap (>= 0.8, < 2.0)
       netrc (~> 0.11)
     cocoapods-try (1.1.0)
@@ -48,9 +53,11 @@ GEM
     fourflusher (2.3.1)
     fuzzy_match (2.0.4)
     gh_inspector (1.1.3)
+    httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    minitest (5.11.3)
+    json (2.2.0)
+    minitest (5.12.0)
     molinillo (0.6.6)
     nanaimo (0.2.6)
     nap (1.1.0)
@@ -59,7 +66,7 @@ GEM
     thread_safe (0.3.6)
     tzinfo (1.2.5)
       thread_safe (~> 0.1)
-    xcodeproj (1.11.0)
+    xcodeproj (1.12.0)
       CFPropertyList (>= 2.3.3, < 4.0)
       atomos (~> 0.1.3)
       claide (>= 1.0.2, < 2.0)
diff --git a/pkgs/development/mobile/cocoapods/gemset-beta.nix b/pkgs/development/mobile/cocoapods/gemset-beta.nix
index e2d4127ae44..f5f95db3ced 100644
--- a/pkgs/development/mobile/cocoapods/gemset-beta.nix
+++ b/pkgs/development/mobile/cocoapods/gemset-beta.nix
@@ -16,10 +16,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1vlasxdgz49y75p8vjkbdpb4kmc73xv71d7vpn9x9xjgvsar03kp";
+      sha256 = "1ayg8j3819ay2d8618jv32ca16fh8qsgjsiq9j32yd016c170nkj";
       type = "gem";
     };
-    version = "1.26.1";
+    version = "1.27.1";
   };
   atomos = {
     groups = ["default"];
@@ -57,10 +57,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1qsj34czqsy93w2bnwhdhr0cyzjwl7vy3sknmak4syyni6m0rlli";
+      sha256 = "108zj698l44wnc0jgx81gxra86c7mrzyqrx6rxssalrc5rviadw7";
       type = "gem";
     };
-    version = "1.8.0.beta.2";
+    version = "1.8.1";
   };
   cocoapods-core = {
     dependencies = ["activesupport" "algoliasearch" "concurrent-ruby" "fuzzy_match" "nap"];
@@ -68,10 +68,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "166pr9m3da9hsra9rviaxz3i4spm7kl003mkn7sn25r9smcvfdj4";
+      sha256 = "15bcc7771jws4p3n3sd26faxslah0yvqgpb0y8gh6d0dwjdygmk0";
       type = "gem";
     };
-    version = "1.8.0.beta.2";
+    version = "1.8.1";
   };
   cocoapods-deintegrate = {
     groups = ["default"];
@@ -130,10 +130,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1m0p27aij7d0n0b8h7nvyv3q3prcpwisbj7sla0fp2hvn4lqarl5";
+      sha256 = "0vrwsgaq3nf7v3pwksgqy0mhswrp3ipczrc96vl3ii2pcc9ilwkw";
       type = "gem";
     };
-    version = "1.4.0";
+    version = "1.4.1";
   };
   cocoapods-try = {
     groups = ["default"];
@@ -241,10 +241,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0icglrhghgwdlnzzp4jf76b0mbc71s80njn5afyfjn4wqji8mqbq";
+      sha256 = "1kj5m8gg643w8jh8nsdy15bpddmnnafhyzhjx7gp28l1acb4fik7";
       type = "gem";
     };
-    version = "5.11.3";
+    version = "5.12.0";
   };
   molinillo = {
     groups = ["default"];
diff --git a/pkgs/development/mobile/cocoapods/gemset.nix b/pkgs/development/mobile/cocoapods/gemset.nix
index 003c3a1bc13..2eb630e0f93 100644
--- a/pkgs/development/mobile/cocoapods/gemset.nix
+++ b/pkgs/development/mobile/cocoapods/gemset.nix
@@ -10,6 +10,17 @@
     };
     version = "4.2.11.1";
   };
+  algoliasearch = {
+    dependencies = ["httpclient" "json"];
+    groups = ["default"];
+    platforms = [];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1ayg8j3819ay2d8618jv32ca16fh8qsgjsiq9j32yd016c170nkj";
+      type = "gem";
+    };
+    version = "1.27.1";
+  };
   atomos = {
     source = {
       remotes = ["https://rubygems.org"];
@@ -19,20 +30,24 @@
     version = "0.1.3";
   };
   CFPropertyList = {
+    groups = ["default"];
+    platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0ykjag3k5msz3sf1j91rb55da2xh596y06m3a4yl79fiy2id0w9z";
+      sha256 = "0fr8sdzs2q1969zqh790w223hjidlwx4hfm4c91gj0va5j5pv3n8";
       type = "gem";
     };
-    version = "3.0.0";
+    version = "3.0.1";
   };
   claide = {
+    groups = ["default"];
+    platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0az54rp691hc42yl1xyix2cxv58byhaaf4gxbpghvvq29l476rzc";
+      sha256 = "0kasxsms24fgcdsq680nz99d5lazl9rmz1qkil2y5gbbssx89g0z";
       type = "gem";
     };
-    version = "1.0.2";
+    version = "1.0.3";
   };
   cocoapods = {
     dependencies = ["activesupport" "claide" "cocoapods-core" "cocoapods-deintegrate" "cocoapods-downloader" "cocoapods-plugins" "cocoapods-search" "cocoapods-stats" "cocoapods-trunk" "cocoapods-try" "colored2" "escape" "fourflusher" "gh_inspector" "molinillo" "nap" "ruby-macho" "xcodeproj"];
@@ -40,21 +55,21 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "02gnm6l7f3pxmy7bqns0dhxmanlqp01hkpvng5cxryww17zrq2qz";
+      sha256 = "108zj698l44wnc0jgx81gxra86c7mrzyqrx6rxssalrc5rviadw7";
       type = "gem";
     };
-    version = "1.7.5";
+    version = "1.8.1";
   };
   cocoapods-core = {
-    dependencies = ["activesupport" "fuzzy_match" "nap"];
+    dependencies = ["activesupport" "algoliasearch" "concurrent-ruby" "fuzzy_match" "nap"];
     groups = ["default"];
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1i53x5lhlvyirls2ch45x9wsrfqk7s3zp85lbnwps9abimxj4nh4";
+      sha256 = "15bcc7771jws4p3n3sd26faxslah0yvqgpb0y8gh6d0dwjdygmk0";
       type = "gem";
     };
-    version = "1.7.5";
+    version = "1.8.1";
   };
   cocoapods-deintegrate = {
     groups = ["default"];
@@ -105,12 +120,14 @@
   };
   cocoapods-trunk = {
     dependencies = ["nap" "netrc"];
+    groups = ["default"];
+    platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1plssgabdv6hcaq1c3gf43kf1d2prx883q8lzdr6chi5byzzs3yl";
+      sha256 = "0vrwsgaq3nf7v3pwksgqy0mhswrp3ipczrc96vl3ii2pcc9ilwkw";
       type = "gem";
     };
-    version = "1.3.1";
+    version = "1.4.1";
   };
   cocoapods-try = {
     source = {
@@ -172,6 +189,16 @@
     };
     version = "1.1.3";
   };
+  httpclient = {
+    groups = ["default"];
+    platforms = [];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "19mxmvghp7ki3klsxwrlwr431li7hm1lczhhj8z4qihl2acy8l99";
+      type = "gem";
+    };
+    version = "2.8.3";
+  };
   i18n = {
     dependencies = ["concurrent-ruby"];
     source = {
@@ -181,13 +208,25 @@
     };
     version = "0.9.5";
   };
+  json = {
+    groups = ["default"];
+    platforms = [];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0sx97bm9by389rbzv8r1f43h06xcz8vwi3h5jv074gvparql7lcx";
+      type = "gem";
+    };
+    version = "2.2.0";
+  };
   minitest = {
+    groups = ["default"];
+    platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0icglrhghgwdlnzzp4jf76b0mbc71s80njn5afyfjn4wqji8mqbq";
+      sha256 = "1kj5m8gg643w8jh8nsdy15bpddmnnafhyzhjx7gp28l1acb4fik7";
       type = "gem";
     };
-    version = "5.11.3";
+    version = "5.12.0";
   };
   molinillo = {
     source = {
@@ -254,9 +293,9 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1h73ilwyjwyyhj761an3pmicllw50514gxb6b1r4z4klc9rzxw4j";
+      sha256 = "162gwhrl7ppj6hlmnpp1scvy1ylcv5xqk51826v075sckdqjp8c8";
       type = "gem";
     };
-    version = "1.11.0";
+    version = "1.12.0";
   };
 }
\ No newline at end of file
diff --git a/pkgs/development/ocaml-modules/ptmap/default.nix b/pkgs/development/ocaml-modules/ptmap/default.nix
index 91b0d22a852..d6637d23052 100644
--- a/pkgs/development/ocaml-modules/ptmap/default.nix
+++ b/pkgs/development/ocaml-modules/ptmap/default.nix
@@ -1,13 +1,22 @@
 { stdenv, fetchzip, ocaml, findlib, obuild }:
 
-let version = "2.0.3"; in
+let param =
+  if stdenv.lib.versionAtLeast ocaml.version "4.07"
+  then {
+    version = "2.0.4";
+    sha256 = "05a391m1l04zigi6ghywj7f5kxy2w6186221k7711wmg56m94yjw";
+  } else {
+    version = "2.0.3";
+    sha256 = "19xykhqk7q25r1pj8rpfj53j2r9ls8mxi1w5m2wqshrf20gf078h";
+  }
+; in
 
 stdenv.mkDerivation {
-  name = "ocaml${ocaml.version}-ptmap-${version}";
+  name = "ocaml${ocaml.version}-ptmap-${param.version}";
 
   src = fetchzip {
-    url = "https://github.com/backtracking/ptmap/archive/v${version}.tar.gz";
-    sha256 = "19xykhqk7q25r1pj8rpfj53j2r9ls8mxi1w5m2wqshrf20gf078h";
+    url = "https://github.com/backtracking/ptmap/archive/v${param.version}.tar.gz";
+    inherit (param) sha256;
   };
 
   buildInputs = [ ocaml findlib obuild ];
diff --git a/pkgs/development/python-modules/MechanicalSoup/default.nix b/pkgs/development/python-modules/MechanicalSoup/default.nix
index 6c4a2d310da..7882685df4c 100644
--- a/pkgs/development/python-modules/MechanicalSoup/default.nix
+++ b/pkgs/development/python-modules/MechanicalSoup/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "MechanicalSoup";
-  version = "0.11.0";
+  version = "0.12.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0k59wwk75q7nz6i6gynvzhagy02ql0bv7py3qqcwgjw7607yq4i7";
+    sha256 = "1g976rk79apz6rc338zq3ml2yps8hb88nyw3a698d0brm4khd9ir";
   };
 
   checkInputs = [ pytest pytestrunner requests-mock pytestcov ];
diff --git a/pkgs/development/python-modules/aioconsole/default.nix b/pkgs/development/python-modules/aioconsole/default.nix
index aa8ed392934..36a1c1b76e4 100644
--- a/pkgs/development/python-modules/aioconsole/default.nix
+++ b/pkgs/development/python-modules/aioconsole/default.nix
@@ -10,11 +10,11 @@
 # wrapped to be able to find aioconsole and any other packages.
 buildPythonPackage rec {
   pname = "aioconsole";
-  version = "0.1.14";
+  version = "0.1.15";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "f1ddd04050d9be5e93e223a4e9367433436d245f8fe70905f4124bfde2cd3cdd";
+    sha256 = "0gbl08p89959g8dqy2vainppg3kyf948xlh18p7iwk5p0mw5d3j9";
   };
 
   # hardcodes a test dependency on an old version of pytest-asyncio
diff --git a/pkgs/development/python-modules/amqp/default.nix b/pkgs/development/python-modules/amqp/default.nix
index bf008df3832..b8d9e8f2537 100644
--- a/pkgs/development/python-modules/amqp/default.nix
+++ b/pkgs/development/python-modules/amqp/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "amqp";
-  version = "2.5.0";
+  version = "2.5.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1j1046gcriidsfha0hvrw6hwcm0wrhbvg0prjjji5inaadyzidnb";
+    sha256 = "0s2yxnnhhx9hww0n33yn22q6sgnbd6n2nw92050qv2qpc3i1ga8r";
   };
 
   checkInputs = [ pytest case pytest-sugar ];
diff --git a/pkgs/development/python-modules/annoy/default.nix b/pkgs/development/python-modules/annoy/default.nix
index ce7d9940bf2..e06f916d5a3 100644
--- a/pkgs/development/python-modules/annoy/default.nix
+++ b/pkgs/development/python-modules/annoy/default.nix
@@ -5,12 +5,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.15.2";
+  version = "1.16.0";
   pname = "annoy";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1i5bkf8mwd1pyrbhfwncir2r8yq8s9qz5j13vv2qz92n9g57sr3m";
+    sha256 = "0jnm38kg7aw63mkd5113i3pb2p9fp5cia91jwhyg9sazb45bzpv9";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/apprise/default.nix b/pkgs/development/python-modules/apprise/default.nix
index 7b8885de169..c2c542a8c01 100644
--- a/pkgs/development/python-modules/apprise/default.nix
+++ b/pkgs/development/python-modules/apprise/default.nix
@@ -1,21 +1,21 @@
 { lib, buildPythonPackage, fetchPypi
-, Babel, decorator, requests, requests_oauthlib, six, click, markdown, pyyaml
+, Babel, requests, requests_oauthlib, six, click, markdown, pyyaml
 , pytestrunner, coverage, flake8, mock, pytest, pytestcov, tox
 }:
 
 buildPythonPackage rec {
   pname = "apprise";
-  version = "0.7.9";
+  version = "0.8.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0zqnk255d311ibird08sv0c21fw1r1xhldhyx5lnl3ji1xkv9173";
+    sha256 = "02apbzckj158995k9ls0gr1m9hfk7nw3ck0bp7k41srl5wdys72i";
   };
 
   nativeBuildInputs = [ Babel ];
 
   propagatedBuildInputs = [
-    decorator requests requests_oauthlib six click markdown pyyaml
+    requests requests_oauthlib six click markdown pyyaml
   ];
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/ase/default.nix b/pkgs/development/python-modules/ase/default.nix
index 643bafe617a..c84672e8abc 100644
--- a/pkgs/development/python-modules/ase/default.nix
+++ b/pkgs/development/python-modules/ase/default.nix
@@ -12,12 +12,12 @@
 
 buildPythonPackage rec {
   pname = "ase";
-  version = "3.18.0";
+  version = "3.18.1";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1ycp1yksysiiz902gn762030sfmirxm950pwpw2rcrpjvq95zm1r";
+    sha256 = "0zxcdj61j9mxlgk2y4ax6rpml9gvmal8aa3pdmwwq4chyzdlh6g2";
   };
 
   propagatedBuildInputs = [ numpy scipy matplotlib flask pillow psycopg2 ];
diff --git a/pkgs/development/python-modules/asgiref/default.nix b/pkgs/development/python-modules/asgiref/default.nix
index 295bc750f82..e75be31c85f 100644
--- a/pkgs/development/python-modules/asgiref/default.nix
+++ b/pkgs/development/python-modules/asgiref/default.nix
@@ -1,6 +1,6 @@
 { stdenv, buildPythonPackage, pythonOlder, fetchFromGitHub, async-timeout, pytest, pytest-asyncio }:
 buildPythonPackage rec {
-  version = "3.2.1";
+  version = "3.2.2";
   pname = "asgiref";
 
   disabled = pythonOlder "3.5";
@@ -10,7 +10,7 @@ buildPythonPackage rec {
     owner = "django";
     repo = pname;
     rev = version;
-    sha256 = "16wb137dvnjmbmshy4r9vgsfjc4g8d6l527aj9d5vszyk5x5fm7d";
+    sha256 = "11lnynspgdi5zp3hd8piy8h9fq0s3ck6lzyl7h0fn2mxxyx83yh2";
   };
 
   propagatedBuildInputs = [ async-timeout ];
diff --git a/pkgs/development/python-modules/asyncssh/default.nix b/pkgs/development/python-modules/asyncssh/default.nix
index ba94e395f67..da222f7e615 100644
--- a/pkgs/development/python-modules/asyncssh/default.nix
+++ b/pkgs/development/python-modules/asyncssh/default.nix
@@ -5,12 +5,12 @@
 
 buildPythonPackage rec {
   pname = "asyncssh";
-  version = "1.17.1";
+  version = "1.18.0";
   disabled = pythonOlder "3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0gyqms4zs9j9k7dgy24va4w42vf20x75yx9jvsds0sg42mqlkd5v";
+    sha256 = "1d9x7xpsqqd5scdk7f1c76lycgrxylaaf5qn4p46i8clfvm5a435";
   };
 
   patches = [
diff --git a/pkgs/development/python-modules/azure-cosmos/default.nix b/pkgs/development/python-modules/azure-cosmos/default.nix
index 2b7c7ded276..72d5b9a6ff7 100644
--- a/pkgs/development/python-modules/azure-cosmos/default.nix
+++ b/pkgs/development/python-modules/azure-cosmos/default.nix
@@ -6,12 +6,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "3.1.0";
+  version = "3.1.1";
   pname = "azure-cosmos";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1955kpn2y16k5mil90bnnyscnh1hyh4d5l5v5b90ms969p61i9zl";
+    sha256 = "0q8pl8wnadxhyawcrfzrm2k85xd4mdmdk2xwdial55zmpa8ji4pk";
   };
 
   propagatedBuildInputs = [ six requests ];
diff --git a/pkgs/development/python-modules/basemap/default.nix b/pkgs/development/python-modules/basemap/default.nix
index 25b19a2b731..a06bcebc8e6 100644
--- a/pkgs/development/python-modules/basemap/default.nix
+++ b/pkgs/development/python-modules/basemap/default.nix
@@ -13,13 +13,13 @@
 
 buildPythonPackage rec {
   pname = "basemap";
-  version = "1.2.0";
+  version = "1.2.1";
 
   src = fetchFromGitHub {
     owner = "matplotlib";
     repo = "basemap";
     rev = "v${version}rel";
-    sha256 = "1p3app8n65rlppkdbp1pb7fa4250kh7hi7lzdsryi2iv88np7193";
+    sha256 = "13lw1iwa8hadpvqdgb06nh881l8c17awzvvwbfwblvb9q9s0lnzp";
   };
 
   propagatedBuildInputs = [ numpy matplotlib pillow pyproj pyshp six ];
diff --git a/pkgs/development/python-modules/bugzilla/default.nix b/pkgs/development/python-modules/bugzilla/default.nix
index 52d42b7a263..a342ac99943 100644
--- a/pkgs/development/python-modules/bugzilla/default.nix
+++ b/pkgs/development/python-modules/bugzilla/default.nix
@@ -3,12 +3,12 @@
 
 buildPythonPackage rec {
   pname = "bugzilla";
-  version = "2.2.0";
+  version = "2.3.0";
 
   src = fetchPypi {
     pname = "python-${pname}";
     inherit version;
-    sha256 = "0x3jjb1g5bgjdj0jf0jmcg80hn5x2isf49frwvf2ykdl3fxd5gxc";
+    sha256 = "0q8c3k0kdnd11g2s56cp8va9365x0xfr2m2zn9fgxjijdyhwdic5";
   };
 
   buildInputs = [ pep8 coverage logilab_common ];
diff --git a/pkgs/development/python-modules/buildbot/default.nix b/pkgs/development/python-modules/buildbot/default.nix
index c19fc280c7f..763362f6bd0 100644
--- a/pkgs/development/python-modules/buildbot/default.nix
+++ b/pkgs/development/python-modules/buildbot/default.nix
@@ -25,11 +25,11 @@ let
 
   package = buildPythonPackage rec {
     pname = "buildbot";
-    version = "2.4.0";
+    version = "2.4.1";
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "141ad2g1j5y0n5cdnd18m55ss0gqjlz5ky85rb6qfn73dgw42vmz";
+      sha256 = "0sqsp7ikmg5v48n1sy7l4913g906hyi1g9sikxd07n8vysp0ncx8";
     };
 
     propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/buildbot/pkg.nix b/pkgs/development/python-modules/buildbot/pkg.nix
index dababe48e99..31723b9537d 100644
--- a/pkgs/development/python-modules/buildbot/pkg.nix
+++ b/pkgs/development/python-modules/buildbot/pkg.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "buildbot-pkg";
-  version = "2.4.0";
+  version = "2.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0na336jwibgbix8fr4jki1gqys44kkm0a8q32llcr2z08igs4mvy";
+    sha256 = "0dfx3b6w9b326a0jrgc42a5ki84ya7bvx10pm62bfcby0mixhd4y";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/buildbot/plugins.nix b/pkgs/development/python-modules/buildbot/plugins.nix
index e31085a2498..e0855bbcb3d 100644
--- a/pkgs/development/python-modules/buildbot/plugins.nix
+++ b/pkgs/development/python-modules/buildbot/plugins.nix
@@ -7,7 +7,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0g3m5z8yska245r1x9n85b4br8b63i4zca2qn3qspf62b1wzmxmd";
+      sha256 = "0l4kyxh62y86cw97101gjs42n1sdw1n18cgh6mm337gzjn42nv3x";
     };
 
     buildInputs = [ buildbot buildbot-pkg mock ];
@@ -26,7 +26,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0p7az9mb09c4bl0j37w28wflzygq9vy8rjbbnhlfbs6py6mjdagr";
+      sha256 = "1s0jl5b9zd7iwxqfb2g145nzf5nx6q44x4y1axkzilkd777162cz";
     };
 
     buildInputs = [ buildbot-pkg ];
@@ -46,7 +46,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0ba0a7q7ii7sipvifxs9ldkcs4b975skndarmirbphc797993hj1";
+      sha256 = "0qld1424d4qvf08qz5ibl3pv0qzj0qxrvgra5dr3wagaq3jfh3kz";
     };
 
     buildInputs = [ buildbot-pkg ];
@@ -66,7 +66,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0dvchhjzmfbbrxqm8dlmwck22z99pgnflxk3cyn0wbb1qskhd9cv";
+      sha256 = "1di8w9dzalg3d2k3wff682irbi8dcksysc9n176zncmkbi2pr2ia";
     };
 
     buildInputs = [ buildbot-pkg ];
@@ -86,7 +86,7 @@
 
     src = fetchPypi {
       inherit pname version;
-      sha256 = "0w9p3y89rqsmqiacwj2avir42r0xjr2yri14v3ay6yar5391r8wa";
+      sha256 = "0gh6ddczlga75n6fh9pkbv39x8p3b6pqviaj287wab27wimd1hxa";
     };
 
     buildInputs = [ buildbot-pkg ];
diff --git a/pkgs/development/python-modules/buildbot/worker.nix b/pkgs/development/python-modules/buildbot/worker.nix
index 8cfc56678c0..ceeb365d1e3 100644
--- a/pkgs/development/python-modules/buildbot/worker.nix
+++ b/pkgs/development/python-modules/buildbot/worker.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage (rec {
   pname = "buildbot-worker";
-  version = "2.4.0";
+  version = "2.4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "04dk1jg0yq0rcm7j7pn7l1pqqjhiyvwppnhc1b7106sx2cdj2yb2";
+    sha256 = "1l2ax9ywrhgrs9f9yyhiq5nhcf34w916ikx6bjcd6f201ixky1xg";
   };
 
   propagatedBuildInputs = [ twisted future ];
diff --git a/pkgs/development/python-modules/bumps/default.nix b/pkgs/development/python-modules/bumps/default.nix
index d8fc3d99235..ccbbf67c596 100644
--- a/pkgs/development/python-modules/bumps/default.nix
+++ b/pkgs/development/python-modules/bumps/default.nix
@@ -2,7 +2,7 @@
 
 buildPythonPackage rec {
   pname = "bumps";
-  version = "0.7.11";
+  version = "0.7.12";
 
   propagatedBuildInputs = [six];
 
@@ -12,7 +12,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "16d24a7f965592d9b02f96e68e6aa70d6fb59abe4db37bb14c4b60c509a3c2ef";
+    sha256 = "0a8m56bwyi0gdrf3kgkdw3cajyxlr40qrj1xlh5yn4qqjbz7ym02";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/cachy/default.nix b/pkgs/development/python-modules/cachy/default.nix
index 029a1864484..d5c3428fcc1 100644
--- a/pkgs/development/python-modules/cachy/default.nix
+++ b/pkgs/development/python-modules/cachy/default.nix
@@ -1,7 +1,7 @@
 { lib, buildPythonPackage, fetchPypi
 , redis
 , memcached
-, msgpack-python
+, msgpack
 }:
 
 buildPythonPackage rec {
@@ -16,7 +16,7 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     redis
     memcached
-    msgpack-python
+    msgpack
   ];
 
   # The Pypi tarball doesn't include tests, and the GitHub source isn't
diff --git a/pkgs/development/python-modules/codespell/default.nix b/pkgs/development/python-modules/codespell/default.nix
index dfd0be09fab..dc531c77fb5 100644
--- a/pkgs/development/python-modules/codespell/default.nix
+++ b/pkgs/development/python-modules/codespell/default.nix
@@ -1,11 +1,11 @@
 { lib, buildPythonApplication, fetchPypi, pytest, chardet }:
 buildPythonApplication rec {
   pname = "codespell";
-  version = "1.15.0";
+  version = "1.16.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0c211rzfgmwls8ab8fj21xp9bhxk6ys3xw8w7chp4arjlifc26wg";
+    sha256 = "1s9dl07ib77gq0iq26mrdpl1c46nkfm7nlhqwxpx5vvs6a1pqfxz";
   };
 
   checkInputs = [ pytest chardet ];
diff --git a/pkgs/development/python-modules/cssselect2/default.nix b/pkgs/development/python-modules/cssselect2/default.nix
index 45a9920dbe2..ff56e2a2f47 100644
--- a/pkgs/development/python-modules/cssselect2/default.nix
+++ b/pkgs/development/python-modules/cssselect2/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "cssselect2";
-  version = "0.2.1";
+  version = "0.2.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "505d2ce3d3a1d390ddb52f7d0864b7efeb115a5b852a91861b498b92424503ab";
+    sha256 = "0skymzb4ncrm2zdsy80f53vi0arf776lvbp51hzh4ayp1il5lj3h";
   };
 
   # We're not interested in code quality tests
diff --git a/pkgs/development/python-modules/datatable/default.nix b/pkgs/development/python-modules/datatable/default.nix
index 200ebef1faa..81a53ac15f4 100644
--- a/pkgs/development/python-modules/datatable/default.nix
+++ b/pkgs/development/python-modules/datatable/default.nix
@@ -1,32 +1,25 @@
-{ blessed
-, buildPythonPackage
-, fetchPypi
-, lib
+{ stdenv, lib, buildPythonPackage, fetchPypi, substituteAll, pythonOlder
+, blessed
+, docutils
 , libcxx
 , libcxxabi
 , llvm
 , openmp
 , pytest
-, pythonOlder
-, stdenv
-, substituteAll
 , typesentry
 }:
 
 buildPythonPackage rec {
   pname = "datatable";
-  version = "0.8.0";
+  version = "0.9.0";
+  disabled = pythonOlder "3.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1s8z81zffrckvdwrrl0pkjc7gsdvjxw59xgg6ck81dl7gkh5grjk";
+    sha256 = "1shwjkm9nyaj6asn57vwdd74pn13pggh14r6dzv729lzxm7nm65f";
   };
 
-  patches = [
-    # Disable the compiler monkey patching, and remove the task that's copying
-    # the native dependencies to the build directory.
-    ./remove-compiler-monkeypatch_disable-native-relocation.patch
-  ] ++ lib.optionals stdenv.isDarwin [
+  patches = lib.optionals stdenv.isDarwin [
     # Replace the library auto-detection with hardcoded paths.
     (substituteAll {
       src = ./hardcode-library-paths.patch;
@@ -37,16 +30,13 @@ buildPythonPackage rec {
     })
   ];
 
-  disabled = pythonOlder "3.5";
-
   propagatedBuildInputs = [ typesentry blessed ];
   buildInputs = [ llvm ] ++ lib.optionals stdenv.isDarwin [ openmp ];
-  checkInputs = [ pytest ];
+  checkInputs = [ docutils pytest ];
 
   LLVM = llvm;
 
   checkPhase = ''
-    # py.test adds local datatable to path, which doesn't contain built native library.
     mv datatable datatable.hidden
     pytest
   '';
diff --git a/pkgs/development/python-modules/datatable/remove-compiler-monkeypatch_disable-native-relocation.patch b/pkgs/development/python-modules/datatable/remove-compiler-monkeypatch_disable-native-relocation.patch
deleted file mode 100644
index 7cdbfa90724..00000000000
--- a/pkgs/development/python-modules/datatable/remove-compiler-monkeypatch_disable-native-relocation.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-diff --git a/setup.py b/setup.py
-index 58fc875..8032561 100644
---- a/setup.py
-+++ b/setup.py
-@@ -141,23 +141,6 @@ if cmd in ("build", "bdist_wheel", "build_ext", "install"):
-     extra_link_args = get_extra_link_args()
-     cpp_files = get_c_sources("c")
- 
--    with TaskContext("Copy dynamic libraries") as log:
--        # Copy system libraries into the datatable/lib folder, so that they can
--        # be packaged with the wheel
--        libs = find_linked_dynamic_libraries()
--        for libpath in libs:
--            trgfile = os.path.join("datatable", "lib",
--                                   os.path.basename(libpath))
--            if os.path.exists(trgfile):
--                log.info("File %s already exists, skipped" % trgfile)
--            else:
--                log.info("Copying %s to %s" % (libpath, trgfile))
--                shutil.copy(libpath, trgfile)
--
--    if ismacos():
--        monkey_patch_compiler()
--
--
- # Create the git version file
- if cmd in ("build", "sdist", "bdist_wheel", "install"):
-     make_git_version_file(True)
diff --git a/pkgs/development/python-modules/django-mailman3/default.nix b/pkgs/development/python-modules/django-mailman3/default.nix
index 91cea9b0059..5702bb226b4 100644
--- a/pkgs/development/python-modules/django-mailman3/default.nix
+++ b/pkgs/development/python-modules/django-mailman3/default.nix
@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "django-mailman3";
-  version = "1.2.0";
+  version = "1.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0v6c1jhcc212wc2xa314irfcchl05r7nysrcy63dcaan958kmnnx";
+    sha256 = "0wppv1q3jkkg2d66qsygc4dfpvhfcj5i2as2xpqnzf3l3w7dgja1";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/django_silk/default.nix b/pkgs/development/python-modules/django_silk/default.nix
index 13ba5ef7964..85e5f8f02f0 100644
--- a/pkgs/development/python-modules/django_silk/default.nix
+++ b/pkgs/development/python-modules/django_silk/default.nix
@@ -23,14 +23,14 @@
 
 buildPythonPackage rec {
   pname = "django-silk";
-  version = "3.0.3";
+  version = "3.0.4";
 
   # pypi tarball doesn't include test project
   src = fetchFromGitHub {
     owner = "jazzband";
     repo = "django-silk";
     rev = version;
-    sha256 = "0j1r88zv7fvmlnrzr2h65czzdcpvl7n847ra1pfc52bfa4lf8b9j";
+    sha256 = "10542yvbchcy8hik2hw3jclb4ic89mxkw0sykag4bw9sv43xv7vx";
   };
   # "test_time_taken" tests aren't suitable for reproducible execution, but django's
   # test runner doesn't have an easy way to ignore tests - so instead prevent it from picking
diff --git a/pkgs/development/python-modules/dkimpy/default.nix b/pkgs/development/python-modules/dkimpy/default.nix
index ef0a6f90741..e4ec38c1a7f 100644
--- a/pkgs/development/python-modules/dkimpy/default.nix
+++ b/pkgs/development/python-modules/dkimpy/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "dkimpy";
-  version = "0.9.2";
+  version = "0.9.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "83d5ddc1b83304dbccba1dc7b9e0ee37bec4269bb9ad5779480991525c3811d6";
+    sha256 = "1rnnax2blmwk6404yrnhswp50xbp2h192rd2l6mra5lh3rg36zvd";
 };
 
   checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/dotnetcore2/default.nix b/pkgs/development/python-modules/dotnetcore2/default.nix
index caafeb54740..c885466f5af 100644
--- a/pkgs/development/python-modules/dotnetcore2/default.nix
+++ b/pkgs/development/python-modules/dotnetcore2/default.nix
@@ -7,7 +7,7 @@
 
 buildPythonPackage rec {
   pname = "dotnetcore2";
-  version = "2.1.8.1";
+  version = "2.1.9";
   format = "wheel";
   disabled = isPy27;
 
@@ -15,7 +15,7 @@ buildPythonPackage rec {
     inherit pname version format;
     python = "py3";
     platform = "manylinux1_x86_64";
-    sha256 = "13zrff5j767d3f8drl397sjhl28winsrfa8pa20svf00xfcsy34s";
+    sha256 = "0h1igixk84md68z7gwj1vd6ki4d5drxh0ih5zww8xcr3qh5r0drb";
   };
 
   nativeBuildInputs = [ unzip ];
diff --git a/pkgs/development/python-modules/dotnetcore2/runtime.patch b/pkgs/development/python-modules/dotnetcore2/runtime.patch
index 54322087a78..28cf10e21d1 100644
--- a/pkgs/development/python-modules/dotnetcore2/runtime.patch
+++ b/pkgs/development/python-modules/dotnetcore2/runtime.patch
@@ -1,7 +1,8 @@
-diff a/dotnetcore2/runtime.py b/dotnetcore2/runtime.py
+diff --git a/dotnetcore2/runtime.py b/dotnetcore2/runtime.py
+index 475e2b4..5b578ec 100644
 --- a/dotnetcore2/runtime.py
 +++ b/dotnetcore2/runtime.py
-@@ -39,13 +39,13 @@ def _get_bin_folder() -> str:
+@@ -41,6 +41,7 @@ def _get_bin_folder() -> str:
  
  
  def get_runtime_path():
@@ -9,6 +10,8 @@ diff a/dotnetcore2/runtime.py b/dotnetcore2/runtime.py
      search_string = os.path.join(_get_bin_folder(), 'dotnet*')
      matches = [f for f in glob.glob(search_string, recursive=True)]
      return matches[0]
+@@ -96,8 +97,7 @@ class _FileLock():
+ 
  
  def ensure_dependencies() -> Optional[str]:
 -    if dist is None:
diff --git a/pkgs/development/python-modules/emoji/default.nix b/pkgs/development/python-modules/emoji/default.nix
index 01cd9190647..5f3d14e73c7 100644
--- a/pkgs/development/python-modules/emoji/default.nix
+++ b/pkgs/development/python-modules/emoji/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "emoji";
-  version = "0.5.3";
+  version = "0.5.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0kn6qq1h0d6cg70wk0hji6bcwg5s18ys6gfmlmfmx8420ka150dn";
+    sha256 = "0x61xypwswhghchp5svs084didkgfwqpq2fbiapvirff5lx2srb0";
   };
 
   checkInputs = [ nose ];
diff --git a/pkgs/development/python-modules/fido2/default.nix b/pkgs/development/python-modules/fido2/default.nix
index 8922d6e0519..08aa2fe7eb2 100644
--- a/pkgs/development/python-modules/fido2/default.nix
+++ b/pkgs/development/python-modules/fido2/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "fido2";
-  version = "0.7.0";
+  version = "0.7.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "11wdcjymw8y6wxgp29gbhdxff3lpc5yp5fcqnr5vnj88g192ic27";
+    sha256 = "10i61g8srx1dk0wfjj11s7ka5pv0661ivwg2r0y3y2nsnf5b90s4";
   };
 
   propagatedBuildInputs = [ six cryptography ];
diff --git a/pkgs/development/python-modules/fx2/default.nix b/pkgs/development/python-modules/fx2/default.nix
index fa5edc1077c..2d47e0669d8 100644
--- a/pkgs/development/python-modules/fx2/default.nix
+++ b/pkgs/development/python-modules/fx2/default.nix
@@ -9,13 +9,13 @@
 
 buildPythonPackage {
   pname = "fx2";
-  version = "unstable-2019-08-27";
+  version = "unstable-2019-09-23";
 
   src = fetchFromGitHub {
     owner = "whitequark";
     repo = "libfx2";
-    rev = "dd1e42c7b46ff410dbb18beab46111bb5491400c";
-    sha256 = "0xvlmx6ym0ylrvnlqzf18d475wa0mfci7wkdbv30gl3hgdhsppjz";
+    rev = "3adb4fc842f174b0686ed122c0309d68356edc11";
+    sha256 = "0b3zp50mschsxi2v3192dmnpw32gwblyl8aswlz9a0vx1qg3ibzn";
   };
 
   nativeBuildInputs = [ sdcc ];
diff --git a/pkgs/development/python-modules/glasgow/default.nix b/pkgs/development/python-modules/glasgow/default.nix
index 264a13aed5e..6e314668fae 100644
--- a/pkgs/development/python-modules/glasgow/default.nix
+++ b/pkgs/development/python-modules/glasgow/default.nix
@@ -1,6 +1,8 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
+, setuptools
+, setuptools_scm
 , sdcc
 , nmigen
 , fx2
@@ -16,19 +18,21 @@
 
 buildPythonPackage rec {
   pname = "glasgow";
-  version = "unstable-2019-08-31";
-  realVersion = lib.substring 0 7 src.rev;
+  version = "unstable-2019-09-28";
+  # python setup.py --version
+  realVersion = "0.1.dev1234+g${lib.substring 0 7 src.rev}";
 
   src = fetchFromGitHub {
     owner = "GlasgowEmbedded";
     repo = "Glasgow";
-    rev = "21641a13c6a0daaf8618aff3c5bfffcb26ef6cca";
-    sha256 = "1dpm1jmm4fg8xf17s6h9g5sc09gq8b6xq955sv2x11nrbqf98l4v";
+    rev = "a1cc0333315847980806fd0330021c6de05c5395";
+    sha256 = "0rdx7fymz828i73bc559sr67aikydz1m8s2a0i6c86gznh1s3cfk";
   };
 
-  nativeBuildInputs = [ sdcc ];
+  nativeBuildInputs = [ setuptools_scm sdcc ];
 
   propagatedBuildInputs = [
+    setuptools
     nmigen
     fx2
     libusb1
@@ -38,20 +42,15 @@ buildPythonPackage rec {
     crcmod
   ];
 
-  postPatch = ''
-    substituteInPlace software/setup.py \
-      --replace 'versioneer.get_version()' '"${realVersion}"'
-  '';
-
   preBuild = ''
     make -C firmware LIBFX2=${fx2}/share/libfx2
     cp firmware/glasgow.ihex software/glasgow
     cd software
+    export SETUPTOOLS_SCM_PRETEND_VERSION="${realVersion}"
   '';
 
-  # a couple failing tests and also installCheck tries to build_ext again
+  # installCheck tries to build_ext again
   doInstallCheck = false;
-  doCheck = false;
 
   checkPhase = ''
     python -m unittest discover
diff --git a/pkgs/development/python-modules/influxdb/default.nix b/pkgs/development/python-modules/influxdb/default.nix
index 657a8178440..d624ebd60e5 100644
--- a/pkgs/development/python-modules/influxdb/default.nix
+++ b/pkgs/development/python-modules/influxdb/default.nix
@@ -9,11 +9,11 @@
 
 buildPythonPackage rec {
   pname = "influxdb";
-  version = "5.2.2";
+  version = "5.2.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0hriag4d4gx4bsqisiz29478sj54b215p6xzmshlw6x9af4z5vxg";
+    sha256 = "0dlddhbmd37qsdfyqn9w3xx4v07hladj6fvk9i15jxmz0iz6q9rh";
   };
 
   # ImportError: No module named tests
diff --git a/pkgs/development/python-modules/intake/default.nix b/pkgs/development/python-modules/intake/default.nix
index f89b7ab1ce6..f670d8f01e0 100644
--- a/pkgs/development/python-modules/intake/default.nix
+++ b/pkgs/development/python-modules/intake/default.nix
@@ -7,7 +7,7 @@
 , hvplot
 , jinja2
 , msgpack-numpy
-, msgpack-python
+, msgpack
 , numpy
 , pandas
 , panel
@@ -39,7 +39,7 @@ buildPythonPackage rec {
     hvplot
     jinja2
     msgpack-numpy
-    msgpack-python
+    msgpack
     numpy
     pandas
     panel
diff --git a/pkgs/development/python-modules/jupytext/default.nix b/pkgs/development/python-modules/jupytext/default.nix
index ae6796825f1..c0b89ddddbd 100644
--- a/pkgs/development/python-modules/jupytext/default.nix
+++ b/pkgs/development/python-modules/jupytext/default.nix
@@ -7,11 +7,11 @@
 
 buildPythonPackage rec {
   pname = "jupytext";
-  version = "1.2.1";
+  version = "1.2.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "05vwxgjh7pzxgdzj0775562bfps8j7w3p7dcf1zfh169whqw9vg8";
+    sha256 = "0a2c00bncf68havs3msra6jkx8frbv3yal56mk85wnkwhzlahj0c";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/kubernetes/default.nix b/pkgs/development/python-modules/kubernetes/default.nix
index 8ba7b109264..153398bdd8e 100644
--- a/pkgs/development/python-modules/kubernetes/default.nix
+++ b/pkgs/development/python-modules/kubernetes/default.nix
@@ -4,7 +4,7 @@
 
 buildPythonPackage rec {
   pname = "kubernetes";
-  version = "10.0.0";
+  version = "10.0.1";
 
   prePatch = ''
     sed -e 's/sphinx>=1.2.1,!=1.3b1,<1.4 # BSD/sphinx/' -i test-requirements.txt
@@ -23,7 +23,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0v3hiy427ca010k8brys3aafgb5013i32yva1nmiibk3xcf7f90f";
+    sha256 = "14l5mj0yjmqsq084pdh8g8hlagvvjkdylpk6xwfsv5ikcsba8w1p";
   };
 
   checkInputs = [ isort coverage pytest mock sphinx autopep8 pep8 codecov recommonmark nose ];
diff --git a/pkgs/development/python-modules/lammps-cython/default.nix b/pkgs/development/python-modules/lammps-cython/default.nix
index 501e4adc21d..df2a122d068 100644
--- a/pkgs/development/python-modules/lammps-cython/default.nix
+++ b/pkgs/development/python-modules/lammps-cython/default.nix
@@ -9,7 +9,7 @@
 , pymatgen
 , ase
 , pytestrunner
-, pytest
+, pytest_4
 , pytestcov
 , isPy3k
 , openssh
@@ -26,7 +26,7 @@ buildPythonPackage rec {
   };
 
   buildInputs = [ cython pytestrunner ];
-  checkInputs = [ pytest pytestcov openssh ];
+  checkInputs = [ pytest_4 pytestcov openssh ];
   propagatedBuildInputs = [ mpi4py pymatgen ase numpy ];
 
   preBuild = ''
diff --git a/pkgs/development/python-modules/ldap3/default.nix b/pkgs/development/python-modules/ldap3/default.nix
index 13fe196e471..58acc263eff 100644
--- a/pkgs/development/python-modules/ldap3/default.nix
+++ b/pkgs/development/python-modules/ldap3/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "ldap3";
-  version = "2.6";
+  version = "2.6.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1f0v82584b7gkzrnnnl4fc88w4i73x7cxqbzy0r0bknm33yfwcq5";
+    sha256 = "0ag5xqlki6pjk3f50b8ar8vynx2fmkna7rfampv3kdgwg8z6gjr7";
   };
 
   propagatedBuildInputs = [ pyasn1 ];
diff --git a/pkgs/development/python-modules/luftdaten/default.nix b/pkgs/development/python-modules/luftdaten/default.nix
index 0138d866ff0..9784d3af61f 100644
--- a/pkgs/development/python-modules/luftdaten/default.nix
+++ b/pkgs/development/python-modules/luftdaten/default.nix
@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "luftdaten";
-  version = "0.6.2";
+  version = "0.6.3";
 
   disabled = !isPy3k;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0919hcycv2rkn99lv4dn78i827mgvm3vagm9xcc6qgawsli8vrlp";
+    sha256 = "161g3s3nwbkn3s101g8l4axll0kk8xxahxnvjrjdg2cghcjq9n8n";
   };
 
   propagatedBuildInputs = [ aiohttp async-timeout ];
diff --git a/pkgs/development/python-modules/mechanize/default.nix b/pkgs/development/python-modules/mechanize/default.nix
index f23c3c9e20b..882872d47e1 100644
--- a/pkgs/development/python-modules/mechanize/default.nix
+++ b/pkgs/development/python-modules/mechanize/default.nix
@@ -2,17 +2,15 @@
 , buildPythonPackage
 , fetchPypi
 , html5lib
-, isPy3k
 }:
 
 buildPythonPackage rec {
   pname = "mechanize";
-  version = "0.4.2";
-  disabled = isPy3k;
+  version = "0.4.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b680ca1b4fabe5ef52024d120f40b8e2ed7d175ed4d67225d2c477dac7c7a58b";
+    sha256 = "1gyxkwjnabqf8xxnkj787xh2dpcnm858g369fnahdcz1wn5hdmyp";
   };
 
   propagatedBuildInputs = [ html5lib ];
@@ -21,7 +19,7 @@ buildPythonPackage rec {
 
   meta = with stdenv.lib; {
     description = "Stateful programmatic web browsing in Python";
-    homepage = http://wwwsearch.sourceforge.net/;
+    homepage = "https://github.com/python-mechanize/mechanize";
     license = "BSD-style";
   };
 
diff --git a/pkgs/development/python-modules/monty/default.nix b/pkgs/development/python-modules/monty/default.nix
index 4675a386054..677cb68ca50 100644
--- a/pkgs/development/python-modules/monty/default.nix
+++ b/pkgs/development/python-modules/monty/default.nix
@@ -5,7 +5,7 @@
 , numpy
 , six
 , ruamel_yaml
-, msgpack-python
+, msgpack
 , coverage
 , coveralls
 , pymongo
@@ -24,7 +24,7 @@ buildPythonPackage rec {
     sha256 = "0vqaaz0dw0ypl6sfwbycpb0qs3ap04c4ghbggklxih66spdlggh6";
   };
 
-  checkInputs = [ lsof nose numpy msgpack-python coverage coveralls pymongo];
+  checkInputs = [ lsof nose numpy msgpack coverage coveralls pymongo];
   propagatedBuildInputs = [ six ruamel_yaml ];
 
   preCheck = ''
diff --git a/pkgs/development/python-modules/mox3/default.nix b/pkgs/development/python-modules/mox3/default.nix
index 8885401ae5f..480e28dffcb 100644
--- a/pkgs/development/python-modules/mox3/default.nix
+++ b/pkgs/development/python-modules/mox3/default.nix
@@ -13,11 +13,11 @@
 
 buildPythonPackage rec {
   pname = "mox3";
-  version = "0.26.0";
+  version = "0.28.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "b13c0b8459d6fb0688f9a4e70feeec43fa2cca05b727fc01156789596e083bb1";
+    sha256 = "17d4vglb71s96hhi6d30vnkr7g1pahv95igc4sjv857qf278d540";
   };
 
   buildInputs = [ subunit testrepository testtools six ];
diff --git a/pkgs/development/python-modules/netcdf4/default.nix b/pkgs/development/python-modules/netcdf4/default.nix
index d3a1cfe3907..8b847397a3c 100644
--- a/pkgs/development/python-modules/netcdf4/default.nix
+++ b/pkgs/development/python-modules/netcdf4/default.nix
@@ -3,13 +3,13 @@
 }:
 buildPythonPackage rec {
   pname = "netCDF4";
-  version = "1.5.1.2";
+  version = "1.5.2";
 
   disabled = isPyPy;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "161pqb7xc9nj0dlnp6ply8c6zv68y1frq619xqfrpmc9s1932jzk";
+    sha256 = "08l92yzg2cy1zrkxjvwya2kpnmfzgwnvgb925hlrgcp5ga9y2xg0";
   };
 
   checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/nmigen-boards/default.nix b/pkgs/development/python-modules/nmigen-boards/default.nix
index 4151d08b60f..7f4654eab79 100644
--- a/pkgs/development/python-modules/nmigen-boards/default.nix
+++ b/pkgs/development/python-modules/nmigen-boards/default.nix
@@ -2,25 +2,28 @@
 , buildPythonPackage
 , fetchFromGitHub
 , nmigen
+, setuptools
+, setuptools_scm
 }:
 
 buildPythonPackage rec {
   pname = "nmigen-boards";
-  version = "unstable-2019-08-30";
-  realVersion = lib.substring 0 7 src.rev;
+  version = "unstable-2019-09-23";
+  # python setup.py --version
+  realVersion = "0.1.dev55+g${lib.substring 0 7 src.rev}";
 
   src = fetchFromGitHub {
     owner = "m-labs";
     repo = "nmigen-boards";
-    rev = "3b80b3a3749ae8f123ff258a25e81bd21412aed4";
-    sha256 = "01qynxip8bq23jfjc5wjd97vxfvhld2zb8sxphwf0zixrmmyaspi";
+    rev = "b8b2bbaff34c905f2b1094a74b6865961feb2290";
+    sha256 = "00gsdm7qf6gsxqmkgqz1ing1yc0352s14pvw863rdbjbd1bv5r0m";
   };
 
-  propagatedBuildInputs = [ nmigen ];
+  nativeBuildInputs = [ setuptools_scm ];
+  propagatedBuildInputs = [ setuptools nmigen ];
 
-  postPatch = ''
-    substituteInPlace setup.py \
-      --replace 'versioneer.get_version()' '"${realVersion}"'
+  preBuild = ''
+    export SETUPTOOLS_SCM_PRETEND_VERSION="${realVersion}"
   '';
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/nmigen/default.nix b/pkgs/development/python-modules/nmigen/default.nix
index 345ba982b0b..02569e0a81b 100644
--- a/pkgs/development/python-modules/nmigen/default.nix
+++ b/pkgs/development/python-modules/nmigen/default.nix
@@ -2,6 +2,8 @@
 , buildPythonPackage
 , pythonOlder
 , fetchFromGitHub
+, setuptools
+, setuptools_scm
 , pyvcd
 , bitarray
 , jinja2
@@ -19,19 +21,22 @@
 
 buildPythonPackage rec {
   pname = "nmigen";
-  version = "unstable-2019-08-31";
-  realVersion = lib.substring 0 7 src.rev;
+  version = "unstable-2019-09-28";
+  # python setup.py --version
+  realVersion = "0.1.dev689+g${lib.substring 0 7 src.rev}";
 
   src = fetchFromGitHub {
     owner = "m-labs";
     repo = "nmigen";
-    rev = "2e206220462c67aa6ae97f7515a2191440fd61b3";
-    sha256 = "0y3w6vd493jqm9b8ppgwzs02v1al8w1n5gylljlsw70ci7fyk4qa";
+    rev = "a02e3750bfeba44bcaad4c5de8d9eb0ef055d9c6";
+    sha256 = "0m399c2nm7y54q2f0fbkmi4h35csbc2llckm6k9kqdf5qc6355wd";
   };
 
   disabled = pythonOlder "3.6";
 
-  propagatedBuildInputs = [ pyvcd bitarray jinja2 ];
+  nativeBuildInputs = [ setuptools_scm ];
+
+  propagatedBuildInputs = [ setuptools pyvcd bitarray jinja2 ];
 
   checkInputs = [ yosys yices ];
 
@@ -48,14 +53,15 @@ buildPythonPackage rec {
       tool icestorm "icepack" //
       tool trellis "ecppack";
   in ''
-    substituteInPlace setup.py \
-      --replace 'versioneer.get_version()' '"${realVersion}"'
-
     substituteInPlace nmigen/_toolchain.py \
       --replace 'overrides = {}' \
                 'overrides = ${builtins.toJSON toolchainOverrides}'
   '';
 
+  preBuild = ''
+    export SETUPTOOLS_SCM_PRETEND_VERSION="${realVersion}"
+  '';
+
   meta = with lib; {
     description = "A refreshed Python toolbox for building complex digital hardware";
     homepage = https://github.com/m-labs/nmigen;
diff --git a/pkgs/development/python-modules/pelican/default.nix b/pkgs/development/python-modules/pelican/default.nix
index 2dcc3e5b873..cbda650158b 100644
--- a/pkgs/development/python-modules/pelican/default.nix
+++ b/pkgs/development/python-modules/pelican/default.nix
@@ -6,13 +6,13 @@
 
 buildPythonPackage rec {
   pname = "pelican";
-  version = "4.1.0";
+  version = "4.1.1";
 
   src = fetchFromGitHub {
     owner = "getpelican";
     repo = "pelican";
     rev = version;
-    sha256 = "1ww3kc5bzp5q7b23n2vmzqch1z06l7vrscn0h96cscvk45sxc7yz";
+    sha256 = "08lwbkgqdf6qx9vg17qj70k7nz2j34ymlnrc4cbz7xj98cw4ams1";
     # Remove unicode file names which leads to different checksums on HFS+
     # vs. other filesystems because of unicode normalisation.
     extraPostFetch = ''
@@ -31,7 +31,7 @@ buildPythonPackage rec {
     glibcLocales
     # Note: Pelican has to adapt to a changed CLI of pandoc before enabling this
     # again. Compare https://github.com/getpelican/pelican/pull/2252.
-    # Version 4.1.0 is incompatible with our current pandoc version.
+    # Version 4.1.1 is incompatible with our current pandoc version.
     # pandoc
     git
     mock
diff --git a/pkgs/development/python-modules/pgspecial/default.nix b/pkgs/development/python-modules/pgspecial/default.nix
index 8c653ce060a..5c5f342651b 100644
--- a/pkgs/development/python-modules/pgspecial/default.nix
+++ b/pkgs/development/python-modules/pgspecial/default.nix
@@ -2,15 +2,15 @@
 
 buildPythonPackage rec {
   pname = "pgspecial";
-  version = "1.11.5";
+  version = "1.11.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0yvlxv9vy0hbfgf0xcwl7wh5hg6cl86arsv1ip3kvn9znn6x8kgl";
+    sha256 = "0wy1zmd44y0vl0kxx2y53g6lpipmixbwwrg6c2r7rc3nwa0icl7p";
   };
 
-  checkInputs = [ pytest psycopg2 ];
-  propagatedBuildInputs = [ click sqlparse ];
+  checkInputs = [ pytest ];
+  propagatedBuildInputs = [ click sqlparse psycopg2 ];
 
   checkPhase = ''
     find tests -name \*.pyc -delete
diff --git a/pkgs/development/python-modules/plotly/default.nix b/pkgs/development/python-modules/plotly/default.nix
index 5cd6c106826..c12857759dd 100644
--- a/pkgs/development/python-modules/plotly/default.nix
+++ b/pkgs/development/python-modules/plotly/default.nix
@@ -11,11 +11,11 @@
 
 buildPythonPackage rec {
   pname = "plotly";
-  version = "4.1.0";
+  version = "4.1.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "166rscpr9xbs3pwd61mivhlm1gv3chkgpk2cy0fpb86axa7z4cwk";
+    sha256 = "06gjvicl5k0qn8xz2gnqd4akxvd81n16gwssr7gwlnmdic5da30g";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/portalocker/default.nix b/pkgs/development/python-modules/portalocker/default.nix
index 7d536c83782..82be4b8151f 100644
--- a/pkgs/development/python-modules/portalocker/default.nix
+++ b/pkgs/development/python-modules/portalocker/default.nix
@@ -10,12 +10,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.5.0";
+  version = "1.5.1";
   pname = "portalocker";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "08y5k39mn5a7n69wv0hsyjqb51lazs4i4dpxp42nla2lhllnpbyr";
+    sha256 = "08d8vm373fbx90wrql2i7025d4ir54sq8ahx6g1pw9h793zqrn0y";
   };
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/pre-commit/default.nix b/pkgs/development/python-modules/pre-commit/default.nix
index 7b5377cc15a..18b548faf21 100644
--- a/pkgs/development/python-modules/pre-commit/default.nix
+++ b/pkgs/development/python-modules/pre-commit/default.nix
@@ -14,12 +14,12 @@
 
 buildPythonApplication rec {
   pname = "pre-commit";
-  version = "1.18.2";
+  version = "1.18.3";
 
   src = fetchPypi {
     inherit version;
     pname = "pre_commit";
-    sha256 = "1y6gd6nq8mfyjxknrgdryvn1bj5arvwaz2r00h41g054lfg3iki1";
+    sha256 = "0gqzx5n5kps7z45rgydciz0sq1m09b4g49vclhvybi57pn3hag0x";
   };
 
   propagatedBuildInputs = [
diff --git a/pkgs/development/python-modules/premailer/default.nix b/pkgs/development/python-modules/premailer/default.nix
index f19f2dfe265..df9d5801302 100644
--- a/pkgs/development/python-modules/premailer/default.nix
+++ b/pkgs/development/python-modules/premailer/default.nix
@@ -4,11 +4,11 @@
 
 buildPythonPackage rec {
   pname = "premailer";
-  version = "3.3.0";
+  version = "3.6.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "93be4f197e9d2a87a8fe6b5b6a79b64070dbb523108dfaf2a415b4558fc78ec1";
+    sha256 = "08pshx7a110k4ll20x0xhpvyn3kkipkrbgxjjn7ncdxs54ihdhgw";
   };
 
   buildInputs = [ mock nose ];
diff --git a/pkgs/development/python-modules/py3status/default.nix b/pkgs/development/python-modules/py3status/default.nix
index 31d31f714b7..21f1148ba6c 100644
--- a/pkgs/development/python-modules/py3status/default.nix
+++ b/pkgs/development/python-modules/py3status/default.nix
@@ -22,11 +22,11 @@
 
 buildPythonPackage rec {
   pname = "py3status";
-  version = "3.19";
+  version = "3.20";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "10ikvdx39phr7n01qa6y9i5lqg3blv0d6y1pwqniczaf558cfp3l";
+    sha256 = "14p0ikbgy1pgphy00gvi6zpkz2kf5mwmawbdqs0l57s0fzrz7xwz";
   };
 
   doCheck = false;
diff --git a/pkgs/development/python-modules/pymediainfo/default.nix b/pkgs/development/python-modules/pymediainfo/default.nix
index 67318bac9bf..dbed3c7f037 100644
--- a/pkgs/development/python-modules/pymediainfo/default.nix
+++ b/pkgs/development/python-modules/pymediainfo/default.nix
@@ -5,11 +5,11 @@
 
 buildPythonPackage rec {
   pname = "pymediainfo";
-  version = "4.0";
+  version = "4.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1yjs208c34p2xsc0r8vbi264ii5hixh546718n06b7v670glqjir";
+    sha256 = "0mhpxs7vlqx8w75z93dy7nnvx89kwfdjkla03l19an15rlyqyspd";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/pyopencl/default.nix b/pkgs/development/python-modules/pyopencl/default.nix
index 8561cbac1b8..cbe9b111a2c 100644
--- a/pkgs/development/python-modules/pyopencl/default.nix
+++ b/pkgs/development/python-modules/pyopencl/default.nix
@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "pyopencl";
-  version = "2019.1";
+  version = "2019.1.1";
 
   checkInputs = [ pytest ];
   buildInputs = [ opencl-headers ocl-icd pybind11 ];
@@ -25,7 +25,7 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "04ahndgc5aqm3pqix2j4vzn9n3k762ylf3yq55jdbxm5cicz9nx0";
+    sha256 = "0g5n1c8gfqhfrfpzdypzwfj1q1nlqzcfjrx397cs6qqw67mg095k";
   };
 
   # py.test is not needed during runtime, so remove it from `install_requires`
diff --git a/pkgs/development/python-modules/pyscard/default.nix b/pkgs/development/python-modules/pyscard/default.nix
index 06e2690c111..ddd8b0ce295 100644
--- a/pkgs/development/python-modules/pyscard/default.nix
+++ b/pkgs/development/python-modules/pyscard/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchPypi, fetchpatch, buildPythonPackage, swig, pcsclite, PCSC }:
+{ stdenv, fetchPypi, buildPythonPackage, swig, pcsclite, PCSC }:
 
 let
   # Package does not support configuring the pcsc library.
@@ -9,12 +9,12 @@ let
 in
 
 buildPythonPackage rec {
-  version = "1.9.8";
+  version = "1.9.9";
   pname = "pyscard";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "15fh00z1an6r5j7hrz3jlq0rb3jygwf3x4jcwsa008bv8vpcg7gm";
+    sha256 = "082cjkbxadaz2jb4rbhr0mkrirzlqyqhcf3r823qb0q1k50ybgg6";
   };
 
   postPatch = if withApplePCSC then ''
@@ -30,14 +30,6 @@ buildPythonPackage rec {
   NIX_CFLAGS_COMPILE = optionalString (! withApplePCSC)
     "-I ${getDev pcsclite}/include/PCSC";
 
-  # The error message differs depending on the macOS host version.
-  # Since Nix reports a constant host version, but proxies to the
-  # underlying library, it's not possible to determine the correct
-  # expected error message.  This patch allows both errors to be
-  # accepted.
-  # See: https://github.com/LudovicRousseau/pyscard/issues/77
-  patches = optionals withApplePCSC [ ./ignore-macos-bug.patch ];
-
   propagatedBuildInputs = if withApplePCSC then [ PCSC ] else [ pcsclite ];
   nativeBuildInputs = [ swig ];
 
diff --git a/pkgs/development/python-modules/pytesseract/default.nix b/pkgs/development/python-modules/pytesseract/default.nix
index e8146a6fc7f..0f10ed601f7 100644
--- a/pkgs/development/python-modules/pytesseract/default.nix
+++ b/pkgs/development/python-modules/pytesseract/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pytesseract";
-  version = "0.2.9";
+  version = "0.3.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1mjr3pa4fycdsl7xk9s8fpn2vhpgx7mrdnn5h4lyyjhz86195ivg";
+    sha256 = "0n9vasm5fp25fmr9ns9i3bf4kri63s1mvmjgc6q8w7rx840ww7df";
   };
 
   patches = [
diff --git a/pkgs/development/python-modules/python-gnupg/default.nix b/pkgs/development/python-modules/python-gnupg/default.nix
index 728a353cec7..90dee35d290 100644
--- a/pkgs/development/python-modules/python-gnupg/default.nix
+++ b/pkgs/development/python-modules/python-gnupg/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname   = "python-gnupg";
-  version = "0.4.4";
+  version = "0.4.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "45daf020b370bda13a1429c859fcdff0b766c0576844211446f9266cae97fb0e";
+    sha256 = "01gckjhvsmr6kfwfk4qdxm5jz8nq8zilbjhzpzpiab6d96cyalrk";
   };
 
   # Let's make the library default to our gpg binary
diff --git a/pkgs/development/python-modules/spacy/default.nix b/pkgs/development/python-modules/spacy/default.nix
index cdef1b2a9bd..441c656a0e1 100644
--- a/pkgs/development/python-modules/spacy/default.nix
+++ b/pkgs/development/python-modules/spacy/default.nix
@@ -15,12 +15,13 @@
 , regex
 , cymem
 , pathlib
-, msgpack-python
+, msgpack
 , msgpack-numpy
 , jsonschema
 , blis
 , wasabi
 , srsly
+, setuptools
 }:
 
 buildPythonPackage rec {
@@ -49,12 +50,13 @@ buildPythonPackage rec {
    requests
    regex
    ftfy
-   msgpack-python
+   msgpack
    msgpack-numpy
    jsonschema
    blis
    wasabi
    srsly
+   setuptools
   ] ++ lib.optional (pythonOlder "3.4") pathlib;
 
   checkInputs = [
diff --git a/pkgs/development/python-modules/thinc/default.nix b/pkgs/development/python-modules/thinc/default.nix
index ac8ab3fd864..945da85b9fa 100644
--- a/pkgs/development/python-modules/thinc/default.nix
+++ b/pkgs/development/python-modules/thinc/default.nix
@@ -8,7 +8,7 @@
 , cymem
 , darwin
 , msgpack-numpy
-, msgpack-python
+, msgpack
 , preshed
 , numpy
 , murmurhash
@@ -44,7 +44,7 @@ buildPythonPackage rec {
    cython
    cymem
    msgpack-numpy
-   msgpack-python
+   msgpack
    preshed
    numpy
    murmurhash
diff --git a/pkgs/development/python-modules/twilio/default.nix b/pkgs/development/python-modules/twilio/default.nix
index b2bb8a740a8..657d98722a2 100644
--- a/pkgs/development/python-modules/twilio/default.nix
+++ b/pkgs/development/python-modules/twilio/default.nix
@@ -3,13 +3,13 @@
 
 buildPythonPackage rec {
   pname = "twilio";
-  version = "6.29.1";
+  version = "6.29.3";
   # tests not included in PyPi, so fetch from github instead
   src = fetchFromGitHub {
     owner = "twilio";
     repo = "twilio-python";
     rev = version;
-    sha256 = "1g2wdy62w25sjibggr25b3833x0fhc7w6ypy8g1fgix217rja7pz";
+    sha256 = "0xc0lw6js8icshjh65rvgbnxrscqsd7ls3h0ni4xqg0kin9wyz42";
   };
 
   buildInputs = [ nose mock ];
diff --git a/pkgs/development/python-modules/whichcraft/default.nix b/pkgs/development/python-modules/whichcraft/default.nix
index 102496582a0..de6c4c570cc 100644
--- a/pkgs/development/python-modules/whichcraft/default.nix
+++ b/pkgs/development/python-modules/whichcraft/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "whichcraft";
-  version = "0.6.0";
+  version = "0.6.1";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1614vs0iwm9abina70vgvxaabi8xbz83yxgqfqi1syrzrhaalk6m";
+    sha256 = "11yfkzyplizdgndy34vyd5qlmr1n5mxis3a3svxmx8fnccdvknxc";
   };
 
   LC_ALL="en_US.utf-8";
diff --git a/pkgs/development/python-modules/zerorpc/default.nix b/pkgs/development/python-modules/zerorpc/default.nix
index 2ad01586189..343c7c6e251 100644
--- a/pkgs/development/python-modules/zerorpc/default.nix
+++ b/pkgs/development/python-modules/zerorpc/default.nix
@@ -1,15 +1,15 @@
-{ lib, buildPythonPackage, fetchPypi, future, gevent, msgpack-python, pyzmq }:
+{ lib, buildPythonPackage, fetchPypi, future, gevent, msgpack, pyzmq }:
 
 buildPythonPackage rec {
   pname = "zerorpc";
-  version = "0.6.1";
+  version = "0.6.3";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "14d0nmprs0nm17d8kg2f7qalsi8x7c4damsccqgncylj7mpnk9hh";
+    sha256 = "d2ee247a566fc703f29c277d767f6f61f1e12f76d0402faea4bd815f32cbf37f";
   };
 
-  propagatedBuildInputs = [ future gevent msgpack-python pyzmq ];
+  propagatedBuildInputs = [ future gevent msgpack pyzmq ];
 
   doCheck = false; # pypi version doesn't include tests
 
diff --git a/pkgs/development/tools/analysis/tflint/default.nix b/pkgs/development/tools/analysis/tflint/default.nix
index 39e9830dd5d..342600c7caa 100644
--- a/pkgs/development/tools/analysis/tflint/default.nix
+++ b/pkgs/development/tools/analysis/tflint/default.nix
@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "tflint";
-  version = "0.11.2";
+  version = "0.12.0";
 
   src = fetchFromGitHub {
     owner = "wata727";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1lhg81bsmzxs46329rlayf8k2y7fbjlmxj09rqbygr9f0693rzgy";
+    sha256 = "1dma1nav6z9919lj4f7cqcf8h12l4gbwn24323y18l57zv988331";
   };
 
-  modSha256 = "10za02363yglhj0pbsd2591rflrrcq12gxx9d53pg9hb7lrxj9ij";
+  modSha256 = "1xjxaszpxv9k9s27y1i54cnp0ip47bq4ad2ziq7n8nb76zxw03mx";
 
   subPackages = [ "." ];
 
diff --git a/pkgs/development/tools/database/sqlitebrowser/default.nix b/pkgs/development/tools/database/sqlitebrowser/default.nix
index 7813eba0436..aa29277281d 100644
--- a/pkgs/development/tools/database/sqlitebrowser/default.nix
+++ b/pkgs/development/tools/database/sqlitebrowser/default.nix
@@ -1,25 +1,20 @@
 { mkDerivation, lib, fetchFromGitHub, cmake, antlr
-, qtbase, qttools, sqlite }:
+, qtbase, qttools, qscintilla, sqlite }:
 
 mkDerivation rec {
-  version = "3.11.2";
   pname = "sqlitebrowser";
+  version = "3.11.2";
 
   src = fetchFromGitHub {
-    repo   = pname;
     owner  = pname;
+    repo   = pname;
     rev    = "v${version}";
     sha256 = "0ydd5fg76d5d23byac1f7f8mzx3brmd0cnnkd58qpmlzi7p9hcvx";
   };
 
-  buildInputs = [ qtbase sqlite ];
-
-  nativeBuildInputs = [ cmake antlr qttools ];
+  buildInputs = [ antlr qtbase qscintilla sqlite ];
 
-  # Use internal `qscintilla` rather than our package to fix the build
-  # (https://github.com/sqlitebrowser/sqlitebrowser/issues/1348#issuecomment-374170936).
-  # This can probably be removed when https://github.com/NixOS/nixpkgs/pull/56034 is merged.
-  cmakeFlags = [ "-DFORCE_INTERNAL_QSCINTILLA=ON" ];
+  nativeBuildInputs = [ cmake qttools ];
 
   NIX_LDFLAGS = [
     "-lQt5PrintSupport"
@@ -32,6 +27,6 @@ mkDerivation rec {
     homepage = http://sqlitebrowser.org/;
     license = licenses.gpl3;
     maintainers = with maintainers; [ ma27 ];
-    platforms = platforms.linux; # can only test on linux
+    platforms = platforms.unix;
   };
 }
diff --git a/pkgs/development/tools/icestorm/default.nix b/pkgs/development/tools/icestorm/default.nix
index b3ce4f8f6a7..a7af74a8dc8 100644
--- a/pkgs/development/tools/icestorm/default.nix
+++ b/pkgs/development/tools/icestorm/default.nix
@@ -11,7 +11,7 @@
 
 stdenv.mkDerivation rec {
   pname = "icestorm";
-  version = "2019.08.31";
+  version = "2019.09.13";
 
   pythonPkg = if usePyPy then pypy3 else python3;
   pythonInterp = pythonPkg.interpreter;
@@ -19,8 +19,8 @@ stdenv.mkDerivation rec {
   src = fetchFromGitHub {
     owner  = "cliffordwolf";
     repo   = "icestorm";
-    rev    = "04f1eb78ed8fd50516aee50102675041a8fd40cd";
-    sha256 = "10jdiw4mw0afcjq7xl3xs8z733mlrx927x620vs2yz91p757jxbd";
+    rev    = "0ec00d892a91cc68e45479b46161f649caea2933";
+    sha256 = "1qlh99fafb7xga702k64fmc9m700nsddrfgcq4x8qn8fplsb64f1";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/development/tools/jazzy/Gemfile.lock b/pkgs/development/tools/jazzy/Gemfile.lock
index 28bd27ecc76..65716e824f9 100644
--- a/pkgs/development/tools/jazzy/Gemfile.lock
+++ b/pkgs/development/tools/jazzy/Gemfile.lock
@@ -7,18 +7,21 @@ GEM
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
+    algoliasearch (1.27.1)
+      httpclient (~> 2.8, >= 2.8.3)
+      json (>= 1.5.1)
     atomos (0.1.3)
     claide (1.0.3)
-    cocoapods (1.7.5)
+    cocoapods (1.8.0)
       activesupport (>= 4.0.2, < 5)
       claide (>= 1.0.2, < 2.0)
-      cocoapods-core (= 1.7.5)
+      cocoapods-core (= 1.8.0)
       cocoapods-deintegrate (>= 1.0.3, < 2.0)
       cocoapods-downloader (>= 1.2.2, < 2.0)
       cocoapods-plugins (>= 1.0.0, < 2.0)
       cocoapods-search (>= 1.0.0, < 2.0)
       cocoapods-stats (>= 1.0.0, < 2.0)
-      cocoapods-trunk (>= 1.3.1, < 2.0)
+      cocoapods-trunk (>= 1.4.0, < 2.0)
       cocoapods-try (>= 1.1.0, < 2.0)
       colored2 (~> 3.1)
       escape (~> 0.0.4)
@@ -27,9 +30,11 @@ GEM
       molinillo (~> 0.6.6)
       nap (~> 1.0)
       ruby-macho (~> 1.4)
-      xcodeproj (>= 1.10.0, < 2.0)
-    cocoapods-core (1.7.5)
+      xcodeproj (>= 1.11.1, < 2.0)
+    cocoapods-core (1.8.0)
       activesupport (>= 4.0.2, < 6)
+      algoliasearch (~> 1.0)
+      concurrent-ruby (~> 1.0)
       fuzzy_match (~> 2.0.4)
       nap (~> 1.0)
     cocoapods-deintegrate (1.0.4)
@@ -38,7 +43,7 @@ GEM
       nap
     cocoapods-search (1.0.0)
     cocoapods-stats (1.1.0)
-    cocoapods-trunk (1.4.0)
+    cocoapods-trunk (1.4.1)
       nap (>= 0.8, < 2.0)
       netrc (~> 0.11)
     cocoapods-try (1.1.0)
@@ -49,9 +54,10 @@ GEM
     fourflusher (2.3.1)
     fuzzy_match (2.0.4)
     gh_inspector (1.1.3)
+    httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    jazzy (0.11.1)
+    jazzy (0.11.2)
       cocoapods (~> 1.5)
       mustache (~> 1.1)
       open4
@@ -60,8 +66,9 @@ GEM
       sassc (~> 2.1)
       sqlite3 (~> 1.3)
       xcinvoke (~> 0.3.0)
+    json (2.2.0)
     liferaft (0.0.6)
-    minitest (5.11.3)
+    minitest (5.12.0)
     molinillo (0.6.6)
     mustache (1.1.0)
     nanaimo (0.2.6)
diff --git a/pkgs/development/tools/jazzy/gemset.nix b/pkgs/development/tools/jazzy/gemset.nix
index 19ec06b6a2b..c397c2a50e2 100644
--- a/pkgs/development/tools/jazzy/gemset.nix
+++ b/pkgs/development/tools/jazzy/gemset.nix
@@ -10,6 +10,17 @@
     };
     version = "4.2.11.1";
   };
+  algoliasearch = {
+    dependencies = ["httpclient" "json"];
+    groups = ["default"];
+    platforms = [];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "1ayg8j3819ay2d8618jv32ca16fh8qsgjsiq9j32yd016c170nkj";
+      type = "gem";
+    };
+    version = "1.27.1";
+  };
   atomos = {
     groups = ["default"];
     platforms = [];
@@ -46,21 +57,21 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "02gnm6l7f3pxmy7bqns0dhxmanlqp01hkpvng5cxryww17zrq2qz";
+      sha256 = "07kwhlf8s5by0bwl07f8nyz0k1szgi801cb51n8wbargwhqk1xa4";
       type = "gem";
     };
-    version = "1.7.5";
+    version = "1.8.0";
   };
   cocoapods-core = {
-    dependencies = ["activesupport" "fuzzy_match" "nap"];
+    dependencies = ["activesupport" "algoliasearch" "concurrent-ruby" "fuzzy_match" "nap"];
     groups = ["default"];
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1i53x5lhlvyirls2ch45x9wsrfqk7s3zp85lbnwps9abimxj4nh4";
+      sha256 = "1clmsmc7407namv0b6d0zssjzamwvvb2k8hxggwmrcbs2gmd20ad";
       type = "gem";
     };
-    version = "1.7.5";
+    version = "1.8.0";
   };
   cocoapods-deintegrate = {
     groups = ["default"];
@@ -115,10 +126,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1m0p27aij7d0n0b8h7nvyv3q3prcpwisbj7sla0fp2hvn4lqarl5";
+      sha256 = "0vrwsgaq3nf7v3pwksgqy0mhswrp3ipczrc96vl3ii2pcc9ilwkw";
       type = "gem";
     };
-    version = "1.4.0";
+    version = "1.4.1";
   };
   cocoapods-try = {
     source = {
@@ -192,6 +203,16 @@
     };
     version = "1.1.3";
   };
+  httpclient = {
+    groups = ["default"];
+    platforms = [];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "19mxmvghp7ki3klsxwrlwr431li7hm1lczhhj8z4qihl2acy8l99";
+      type = "gem";
+    };
+    version = "2.8.3";
+  };
   i18n = {
     dependencies = ["concurrent-ruby"];
     groups = ["default"];
@@ -209,10 +230,20 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0kdja4bhzak79xvfpwwakqsjw07vfg458d62k08a416im7xcfcmc";
+      sha256 = "0dw29rsdijr4dhpvn89m3934qrr80a4jyg3v813iy7jbkb6kspj4";
+      type = "gem";
+    };
+    version = "0.11.2";
+  };
+  json = {
+    groups = ["default"];
+    platforms = [];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "0sx97bm9by389rbzv8r1f43h06xcz8vwi3h5jv074gvparql7lcx";
       type = "gem";
     };
-    version = "0.11.1";
+    version = "2.2.0";
   };
   liferaft = {
     source = {
@@ -227,10 +258,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0icglrhghgwdlnzzp4jf76b0mbc71s80njn5afyfjn4wqji8mqbq";
+      sha256 = "1kj5m8gg643w8jh8nsdy15bpddmnnafhyzhjx7gp28l1acb4fik7";
       type = "gem";
     };
-    version = "5.11.3";
+    version = "5.12.0";
   };
   molinillo = {
     groups = ["default"];
diff --git a/pkgs/development/tools/misc/lsof/default.nix b/pkgs/development/tools/misc/lsof/default.nix
index 1298346ef31..274577c4a4c 100644
--- a/pkgs/development/tools/misc/lsof/default.nix
+++ b/pkgs/development/tools/misc/lsof/default.nix
@@ -34,6 +34,10 @@ stdenv.mkDerivation rec {
   '';
 
   installPhase = ''
+    # Fix references from man page https://github.com/lsof-org/lsof/issues/66
+    substituteInPlace Lsof.8 \
+      --replace ".so ./00DIALECTS" "" \
+      --replace ".so ./version" ".ds VN ${version}"
     mkdir -p $out/bin $out/man/man8
     cp Lsof.8 $out/man/man8/lsof.8
     cp lsof $out/bin
diff --git a/pkgs/development/tools/misc/lttng-ust/default.nix b/pkgs/development/tools/misc/lttng-ust/default.nix
index ad5276e5e1a..4b0be0f0fa4 100644
--- a/pkgs/development/tools/misc/lttng-ust/default.nix
+++ b/pkgs/development/tools/misc/lttng-ust/default.nix
@@ -13,11 +13,11 @@
 
 stdenv.mkDerivation rec {
   pname = "lttng-ust";
-  version = "2.10.4";
+  version = "2.10.5";
 
   src = fetchurl {
     url = "https://lttng.org/files/lttng-ust/${pname}-${version}.tar.bz2";
-    sha256 = "0rx9q5r9qcdx3i9i0rx28p33yl52sd6f35qj7qs4li2w42xv9mbm";
+    sha256 = "0ddwk0nl28bkv2xb78gz16a2bvlpfbjmzwfbgwf5p1cq46dyvy86";
   };
 
   buildInputs = [ python ];
diff --git a/pkgs/development/tools/pet/default.nix b/pkgs/development/tools/pet/default.nix
index 7953a55c7d9..e7f4fce3c4d 100644
--- a/pkgs/development/tools/pet/default.nix
+++ b/pkgs/development/tools/pet/default.nix
@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "pet";
-  version = "0.3.5";
+  version = "0.3.6";
 
   src = fetchFromGitHub {
     owner = "knqyf263";
     repo = "pet";
     rev = "v${version}";
-    sha256 = "03fzvvdmb06kf2zglaf8jkqxqv9h1kl7n586ww61z3n3mmp1x4rd";
+    sha256 = "1na3az7vicjq1rxd3ybid47yrblsdazgli0dchkbwh8zchwhqj33";
   };
 
   modSha256 = "06ham8lsx5c1vk5jkwp1aa9g4q4g7sfq7gxz2gkffa98x2vlawyf";
diff --git a/pkgs/development/tools/trellis/default.nix b/pkgs/development/tools/trellis/default.nix
index c98529484d5..d9ec787fc47 100644
--- a/pkgs/development/tools/trellis/default.nix
+++ b/pkgs/development/tools/trellis/default.nix
@@ -8,16 +8,17 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "trellis";
-  version = "2019.09.01";
+  version = "2019.09.27";
+  # git describe --tags
   realVersion = with stdenv.lib; with builtins;
-    "1.0-53-g${substring 0 7 (elemAt srcs 0).rev}";
+    "1.0-71-g${substring 0 7 (elemAt srcs 0).rev}";
 
   srcs = [
     (fetchFromGitHub {
        owner  = "symbiflow";
        repo   = "prjtrellis";
-       rev    = "98871e0e2959bc8cb4de3c7ebe2b9eddc4efe00c";
-       sha256 = "1yq7ih2xvhfvdpijmbqjq6jcngl6710kiv66hkww5ih8j5dzsq5l";
+       rev    = "06904938dfe8f52392e73f7c8b1e034327887c27";
+       sha256 = "1yk13pipj7wp2mma0qcss4sa0wx8h60x0l0x9awh8g2iyk1y8nfw";
        name   = "trellis";
      })
     (fetchFromGitHub {
@@ -32,11 +33,9 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ boostWithPython3 ];
   nativeBuildInputs = [ cmake python3 ];
+  cmakeFlags = [ "-DCURRENT_GIT_VERSION=${realVersion}" ];
 
   preConfigure = with builtins; ''
-    substituteInPlace libtrellis/CMakeLists.txt \
-      --replace "git describe --tags" "echo ${realVersion}"
-
     rmdir database && ln -sfv ${elemAt srcs 1} ./database
 
     source environment.sh
diff --git a/pkgs/development/tools/wabt/default.nix b/pkgs/development/tools/wabt/default.nix
index f8936e27516..4c7df9b12d8 100644
--- a/pkgs/development/tools/wabt/default.nix
+++ b/pkgs/development/tools/wabt/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "wabt";
-  version = "1.0.11";
+  version = "1.0.12";
 
   src = fetchFromGitHub {
     owner  = "WebAssembly";
     repo   = "wabt";
     rev    = version;
-    sha256 = "0hn88vlqyclpk79v3wg3lrssd9vwhjdgvb41g03jqakygxxgnmp5";
+    sha256 = "1zlv3740wkqj4mn6sr84h0x6wk2lcp4pwwmqsh5yyqp1j1glbsa0";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/games/ivan/default.nix b/pkgs/games/ivan/default.nix
index 86f3f721446..0a7474e0f51 100644
--- a/pkgs/games/ivan/default.nix
+++ b/pkgs/games/ivan/default.nix
@@ -3,13 +3,13 @@
 stdenv.mkDerivation rec {
 
   pname = "ivan";
-  version = "056";
+  version = "057";
 
   src = fetchFromGitHub {
     owner = "Attnam";
     repo = "ivan";
     rev = "v${version}";
-    sha256 = "07mj3b2p3n3bq7rwi31y0vywnr4namqbcnz4c53kl38ajw9viyf0";
+    sha256 = "0mavmwikfsyr5sp65sl8dqknl1yz7c7ds53y1qkma24vsikz3k64";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
diff --git a/pkgs/games/system-syzygy/default.nix b/pkgs/games/system-syzygy/default.nix
new file mode 100644
index 00000000000..ee47bd54506
--- /dev/null
+++ b/pkgs/games/system-syzygy/default.nix
@@ -0,0 +1,43 @@
+{lib, rustPlatform, fetchFromGitHub, fetchurl, SDL2, makeWrapper, makeDesktopItem}:
+
+let
+  desktopFile = makeDesktopItem {
+    name = "system-syzygy";
+    exec = "%out%/bin/syzygy";
+    comment = "A puzzle game";
+    desktopName = "System Syzygy";
+    categories = "Game;";
+  };
+in
+rustPlatform.buildRustPackage rec {
+  pname = "system-syzygy";
+  version = "1.0.1";
+
+  src = fetchFromGitHub {
+    owner = "mdsteele";
+    repo = "syzygy";
+    rev = "5ba148fed7aae14bf35108d7303e4194e8ffe5e8";
+    sha256 = "07mzwx8ql33q865snnw4gm3dgf0mnm60lnq1f5fgas2yjy9g9vwa";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ SDL2 ];
+
+  cargoSha256 = "03724z33dqxbbrzpvz172qh45qrgnyb801algjdcm32v8xsx81qg";
+
+  postInstall = ''
+    mkdir -p $out/share/syzygy/
+    cp -r ${src}/data/* $out/share/syzygy/
+    wrapProgram $out/bin/syzygy --set SYZYGY_DATA_DIR $out/share/syzygy
+    mkdir -p $out/share/applications
+    substituteAll ${desktopFile}/share/applications/system-syzygy.desktop $out/share/applications/system-syzygy.desktop
+  '';
+
+
+  meta = with lib; {
+    description = "A story and a puzzle game, where you solve a variety of puzzle";
+    homepage = "https://mdsteele.games/syzygy";
+    license = licenses.gpl3Plus;
+    maintainers = [ maintainers.marius851000 ];
+  };
+}
diff --git a/pkgs/misc/vim-plugins/generated.nix b/pkgs/misc/vim-plugins/generated.nix
index be1e6427bee..5f354491691 100644
--- a/pkgs/misc/vim-plugins/generated.nix
+++ b/pkgs/misc/vim-plugins/generated.nix
@@ -61,12 +61,12 @@ let
 
   ale = buildVimPluginFrom2Nix {
     pname = "ale";
-    version = "2019-09-20";
+    version = "2019-09-25";
     src = fetchFromGitHub {
       owner = "w0rp";
       repo = "ale";
-      rev = "ab8e0433536dc6074c77f6ed1fa18325ea1be349";
-      sha256 = "0nlpcph9f0sfx50rvzdc2vz6b23x2hgx46ywjflfix54cmakpkl8";
+      rev = "41ff80dc9ec2cc834cc8c4aaa753e308223d48b8";
+      sha256 = "1bfylcp9490cd2yz00nq6ky1w55dkvldrdjxip36ahci4cpfn0xw";
     };
   };
 
@@ -83,12 +83,12 @@ let
 
   ansible-vim = buildVimPluginFrom2Nix {
     pname = "ansible-vim";
-    version = "2019-09-15";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "pearofducks";
       repo = "ansible-vim";
-      rev = "95531d40e5c5a6417aac53b7d4e8bd7130d5efe6";
-      sha256 = "1xa8hh95am0baxrjm411fdpzmf3mkkfcpb56cxr81n9idmq1qlqp";
+      rev = "ac2e4f55aedddd7f473aaaa4035062c3c489e8c3";
+      sha256 = "0kgdm06g67y3pfzcd4wqdrc59klxchrim755ml1038hbnk39lilj";
     };
   };
 
@@ -105,12 +105,12 @@ let
 
   auto-git-diff = buildVimPluginFrom2Nix {
     pname = "auto-git-diff";
-    version = "2019-01-21";
+    version = "2019-09-23";
     src = fetchFromGitHub {
       owner = "hotwatermorning";
       repo = "auto-git-diff";
-      rev = "1be2fec036f747fe44ec7f0a3868af0b0980954f";
-      sha256 = "1yvbz4pn73j8jyarjbwidr88zg7vw3gq3hvh4334148iq2fj8529";
+      rev = "a14d52b7ed7e7fb69bf1de9d363f3abdd3410b3a";
+      sha256 = "0i0bnlxclh8pzanrxj428728mdx4wdy19fx499kiin87qr4r2hbn";
     };
   };
 
@@ -314,12 +314,12 @@ let
 
   coc-go = buildVimPluginFrom2Nix {
     pname = "coc-go";
-    version = "2019-09-16";
+    version = "2019-09-24";
     src = fetchFromGitHub {
       owner = "josa42";
       repo = "coc-go";
-      rev = "3c7954c3e167ca3785efb96d3e95563b7e0d4045";
-      sha256 = "0nir8yvqrz2a8zmjp8ny4s08qlcvy3ms6k55i21xvyjwyrmrknpq";
+      rev = "a03314978c6b94701ddfd614f70e52d63bfd4540";
+      sha256 = "1awshnwsvrdxmh0xd1yqp3vnsva93i89frss0gym1szv15697j2q";
     };
   };
 
@@ -380,12 +380,12 @@ let
 
   coc-json = buildVimPluginFrom2Nix {
     pname = "coc-json";
-    version = "2019-09-12";
+    version = "2019-09-22";
     src = fetchFromGitHub {
       owner = "neoclide";
       repo = "coc-json";
-      rev = "ad75187c954f55ec3f92ca9ac5d9f77347b0bbfe";
-      sha256 = "0hwv394498qz6bb5zl2i57d18dbl4faxmh3g2d8mfggmx16pv41n";
+      rev = "d47bbf74ccee5954be887845248251eb9b75635e";
+      sha256 = "08xr276n37x8wx5jzka0hw09mx20n4irdcq1mmy89w9p9rh54fgh";
     };
   };
 
@@ -402,12 +402,12 @@ let
 
   coc-neco = buildVimPluginFrom2Nix {
     pname = "coc-neco";
-    version = "2018-12-21";
+    version = "2019-09-23";
     src = fetchFromGitHub {
       owner = "neoclide";
       repo = "coc-neco";
-      rev = "2c33b8b5a9847ff5b4abca37be88131cc4d746ab";
-      sha256 = "10b23y5g16ggb5mrn1f6dv5mr3ncg0wpn8bvn8g22zz4g737nzii";
+      rev = "e6eb1ccc2ab98966fe678107c6da0d4ddfa34f10";
+      sha256 = "14lph4dg7q0s5yjdr8snz9yl7bn6gs42ikizb6mxq43qqfdnxzdx";
     };
   };
 
@@ -424,12 +424,12 @@ let
 
   coc-prettier = buildVimPluginFrom2Nix {
     pname = "coc-prettier";
-    version = "2019-09-16";
+    version = "2019-09-26";
     src = fetchFromGitHub {
       owner = "neoclide";
       repo = "coc-prettier";
-      rev = "5b25fc3a4709c1e0e61f95ec82f039d1b8c426a3";
-      sha256 = "1j4whxna3gjjs29ndlfr9wpzylapa889831yf1pn7lz2847hnjdr";
+      rev = "6e7d0e32ecc60c68f0ebbd3cf26ea6b7c3c95faa";
+      sha256 = "0fxn2p78d16wgy74mb24hnyq63d2wmzv0873yg950cal4xidw644";
     };
   };
 
@@ -545,12 +545,12 @@ let
 
   coc-tsserver = buildVimPluginFrom2Nix {
     pname = "coc-tsserver";
-    version = "2019-09-09";
+    version = "2019-09-23";
     src = fetchFromGitHub {
       owner = "neoclide";
       repo = "coc-tsserver";
-      rev = "30cf468536a47c994133bb0b5614f305dd6441fe";
-      sha256 = "1nkx1wmhmic4xavb5pnssv14cb6k3znc2jlfcc3ipanm0a6bwkpx";
+      rev = "4bd9cde9dc8c623b9486b845f7a5df2f466e70e6";
+      sha256 = "0mqjf4x95sx61h4r80aifpzdzwb6s832g5g0nnz4p2c1gpcckz63";
     };
   };
 
@@ -766,23 +766,23 @@ let
 
   dart-vim-plugin = buildVimPluginFrom2Nix {
     pname = "dart-vim-plugin";
-    version = "2019-09-20";
+    version = "2019-09-24";
     src = fetchFromGitHub {
       owner = "dart-lang";
       repo = "dart-vim-plugin";
-      rev = "27b3ebd24f1c5690700b7f94f112c06216a0dd76";
-      sha256 = "012vg71h0jijhj430dqd38xh2gq5k79zr1m59gvh004jjb8bh8c7";
+      rev = "f8486e58fb02351689ae247cebf28b5fee326c33";
+      sha256 = "038zx5zn4da73ps5klixcwh64z6rivfp78l2lvaj5d1vjqh1ac83";
     };
   };
 
   defx-nvim = buildVimPluginFrom2Nix {
     pname = "defx-nvim";
-    version = "2019-08-19";
+    version = "2019-09-25";
     src = fetchFromGitHub {
       owner = "Shougo";
       repo = "defx.nvim";
-      rev = "dbd2dceea914ecaa71d24a1d6036f1981becdca5";
-      sha256 = "1gl18s39v7k1p6z7hchq1k16f6f1i2ccq76as562c0nvn68jdqi8";
+      rev = "6da0c868fbc8c1fbdc99bb2208d1070c30994cd0";
+      sha256 = "17mm0hjhvcgkwp48lazjrv9g34bi31xr79f1nr3k55q1g0cqb3a4";
     };
   };
 
@@ -821,12 +821,12 @@ let
 
   denite-nvim = buildVimPluginFrom2Nix {
     pname = "denite-nvim";
-    version = "2019-09-19";
+    version = "2019-09-28";
     src = fetchFromGitHub {
       owner = "Shougo";
       repo = "denite.nvim";
-      rev = "a4969dfe9decc6184548b919379ec39027d627c6";
-      sha256 = "0crwjbvflvf5axgqqfj04q67ilgfnhchi0gxbxi152h6hm4f1wx3";
+      rev = "2de8a3dfd7a104ce6e661c672d58f90ffa90dc35";
+      sha256 = "1bnlr0lrkl8djhji0vaplx73vw4yq82nx90lzd9jch1fm4d5mdq0";
     };
   };
 
@@ -934,23 +934,23 @@ let
 
   deoplete-ternjs = buildVimPluginFrom2Nix {
     pname = "deoplete-ternjs";
-    version = "2019-07-09";
+    version = "2019-09-22";
     src = fetchFromGitHub {
       owner = "carlitux";
       repo = "deoplete-ternjs";
-      rev = "fe5935dcf3cbaa663c81e2b9705a93840a407e56";
-      sha256 = "04yqw92yjcvimwvx1dqqc50y52j3y4zkvjkxmpmfnyx86ah730fk";
+      rev = "307f9c3beb178026d122d9ab3825e4640dd1c29a";
+      sha256 = "039qbcg9fanrs7dc52n987rhd0xdyvsmjdrfd1dcrr6ys990n64d";
     };
   };
 
   deoplete-nvim = buildVimPluginFrom2Nix {
     pname = "deoplete-nvim";
-    version = "2019-09-20";
+    version = "2019-09-26";
     src = fetchFromGitHub {
       owner = "Shougo";
       repo = "deoplete.nvim";
-      rev = "7f1d4d8b1f5dbf344f2d0d1f4b8c5d6a0aaa24a6";
-      sha256 = "1i8964nwarq2hwbixbj74n5a5k8c27hn7srbf8bbckk12rh1rjkj";
+      rev = "503c42d17deb812ee5363e271cca0e68856a289d";
+      sha256 = "1b4hd4g3s96gbq3bi4jbry02jhbzvhx09jss574krhp771mrkzl2";
     };
   };
 
@@ -1057,12 +1057,12 @@ let
 
   falcon = buildVimPluginFrom2Nix {
     pname = "falcon";
-    version = "2019-09-17";
+    version = "2019-09-24";
     src = fetchFromGitHub {
       owner = "fenetikm";
       repo = "falcon";
-      rev = "a6ba8a5d6745d92a23eb8b95562bbd9f05f8de5f";
-      sha256 = "0in4fs2aycwyspi1yck36f6w6m9jmjm5ckdq5wxisvjncnzxblhs";
+      rev = "346587418bc7a1b39bdf65dce2a85a1058ed87b5";
+      sha256 = "17qa5xhqjy43sg1nmm83z90dk8nfkd64n98ijx04kqprk6jp90rq";
     };
   };
 
@@ -1090,12 +1090,12 @@ let
 
   ferret = buildVimPluginFrom2Nix {
     pname = "ferret";
-    version = "2019-08-13";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "wincent";
       repo = "ferret";
-      rev = "aeb47b01b36021aaf84ff4f7f1a4cf64bc68fe53";
-      sha256 = "1cssvdpkmrlby50p2lyqfz1jhp5igyv1bqd34588p3ivsd3hrhyy";
+      rev = "d03f7ebeb0cea0311d23888adb1d62efcf04021a";
+      sha256 = "1xh6jp1gzmn211bfv7v1r88sh49x1zly16qs3k70qgj9w57zgwwy";
     };
   };
 
@@ -1410,12 +1410,12 @@ let
 
   jedi-vim = buildVimPluginFrom2Nix {
     pname = "jedi-vim";
-    version = "2019-09-18";
+    version = "2019-09-24";
     src = fetchFromGitHub {
       owner = "davidhalter";
       repo = "jedi-vim";
-      rev = "89c995e7d964fb71c715e6f4ac330e4c59b44128";
-      sha256 = "02ks1bwrdw7zmnf9mipvfjla9cv6904sx18q9qnyrqbkclrpfn0y";
+      rev = "50abb5e95a8d496dbda7b04a9bb78e4a6cd0a968";
+      sha256 = "04zag6ngqa1djwc2yk0p6hwknsm06nl3lvlyymz57vl51nhmvc2c";
       fetchSubmodules = true;
     };
   };
@@ -1730,12 +1730,12 @@ let
 
   neoformat = buildVimPluginFrom2Nix {
     pname = "neoformat";
-    version = "2019-08-26";
+    version = "2019-09-26";
     src = fetchFromGitHub {
       owner = "sbdchd";
       repo = "neoformat";
-      rev = "eb94d083bc0c9a4e4bec8a205fc65f6a464bd0f7";
-      sha256 = "1va2dvqjjlcyl2in9wjh6c8gmnxlnl13j7gmf2g37j6jm28l16r9";
+      rev = "6b66c20fadd489460422104a62279a0cd8b35eda";
+      sha256 = "1kfhirlxq90vbqzg0wwa69aya0k89icxbw8qdinfrsfng1f3yliq";
     };
   };
 
@@ -1840,23 +1840,23 @@ let
 
   nerdcommenter = buildVimPluginFrom2Nix {
     pname = "nerdcommenter";
-    version = "2019-09-20";
+    version = "2019-09-26";
     src = fetchFromGitHub {
       owner = "scrooloose";
       repo = "nerdcommenter";
-      rev = "50f307bbf68e7402a1564689910ec65ae7ab1781";
-      sha256 = "0f3b9vx3lvq8612k1qnsdzbwp2drvy1vj3xqfxvxpzzsay10qcb1";
+      rev = "a4b7c046b3d3e170c6f62a6209abfa0760d6694a";
+      sha256 = "0qz5b00rv59b3ng8wzf69lgbabqxfwzxbcj2595hmyf6pi0k0swz";
     };
   };
 
   nerdtree = buildVimPluginFrom2Nix {
     pname = "nerdtree";
-    version = "2019-09-15";
+    version = "2019-09-26";
     src = fetchFromGitHub {
       owner = "scrooloose";
       repo = "nerdtree";
-      rev = "9193962ad88f15d9f426c3cfb8a274ff1dd0c5b2";
-      sha256 = "1mgi6k3q46za4c8z9nc4rn6pcj4bc9pkvfqbzymwn03pj4r6n8yp";
+      rev = "496b61ead1acd80128164cce5c2ff8e89c42ded2";
+      sha256 = "0d7c6rf8sbfvxfqd79i92gas7rcd9lzfw15iiala3xr74bap5kpb";
     };
   };
 
@@ -1939,12 +1939,12 @@ let
 
   nvimdev-nvim = buildVimPluginFrom2Nix {
     pname = "nvimdev-nvim";
-    version = "2019-09-03";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "neovim";
       repo = "nvimdev.nvim";
-      rev = "83c2a2aab7f2f7ae8c004c52aaddc8b15065ba90";
-      sha256 = "0i0ds5mfx2k03ivncw795xr3p9iig1b4pqj4mbr7b7hs3984jh08";
+      rev = "c405a548d489e3bb93784ecf5f6fa25109305ac1";
+      sha256 = "17n9adnhhc6hnvrw98i54f8jb1510bfzgciwf436l5xgcjgvqvk0";
     };
   };
 
@@ -3171,12 +3171,12 @@ let
 
   vim-devicons = buildVimPluginFrom2Nix {
     pname = "vim-devicons";
-    version = "2019-09-17";
+    version = "2019-09-23";
     src = fetchFromGitHub {
       owner = "ryanoasis";
       repo = "vim-devicons";
-      rev = "0f9146e9fafe3317693ca214a3f68cd1e036424f";
-      sha256 = "086ng0gja855bmh99qcwwvchwk64dgz1kj1j24yapx2ab314w6g8";
+      rev = "fae1550b95f537b879da7ebb7bfaa0ac65859271";
+      sha256 = "1h0x6wck52ga8qq2phk718yn30yniljbhgrvp59qi5fskx8hsjd4";
     };
   };
 
@@ -3204,12 +3204,12 @@ let
 
   vim-dispatch = buildVimPluginFrom2Nix {
     pname = "vim-dispatch";
-    version = "2019-09-20";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "tpope";
       repo = "vim-dispatch";
-      rev = "1f39fa150fc9275ff264e1f8807fc6fcbbdae012";
-      sha256 = "0c1492hh0gldjyd8w3wsyz6py7qw4r2idfjh8klkk39pg9aajwjl";
+      rev = "4bd1ecd7f38206ef26c37d7d142df58c4237d9dc";
+      sha256 = "0wz8p8fm48dbpzd00h9qw0q2s3r7nm8qa5kcligcrzh1kv139026";
     };
   };
 
@@ -3402,12 +3402,12 @@ let
 
   vim-fugitive = buildVimPluginFrom2Nix {
     pname = "vim-fugitive";
-    version = "2019-09-19";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "tpope";
       repo = "vim-fugitive";
-      rev = "1d8c0a38b2fc4ce9ca4204676573b6335725ff75";
-      sha256 = "0ln11qdpsssgqd122zldfmjvwyvxild8a0yxgdazp720dypkvgjm";
+      rev = "ab26e9fdb328cc351933f8d6178178e8ce5c8381";
+      sha256 = "0fvn2y7wyj7i39p027d4ijz73vpidzlgg7g7b9bcvyjsfmyds1fk";
     };
   };
 
@@ -3446,12 +3446,12 @@ let
 
   vim-gitgutter = buildVimPluginFrom2Nix {
     pname = "vim-gitgutter";
-    version = "2019-09-19";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "airblade";
       repo = "vim-gitgutter";
-      rev = "76aa5920dba9b05991940f7dc29dc79ad7af0a3e";
-      sha256 = "0yazz5aqyfkwhx2x44pp8x81wswrh7sjgslbimwa9d67yvnh0bz6";
+      rev = "44bb472bac2fa96c1444fcc02ad981152e56735b";
+      sha256 = "0dcm685sdwaajglh8iv2a20sf47a6lmahj5jscdpcbpnhcd3wdia";
     };
   };
 
@@ -3479,12 +3479,12 @@ let
 
   vim-go = buildVimPluginFrom2Nix {
     pname = "vim-go";
-    version = "2019-09-21";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "fatih";
       repo = "vim-go";
-      rev = "6904ded741573113c20408abdce455c5d3969e08";
-      sha256 = "12ill4rpfc3bzxa6s47mscvbclidnckxci3rdixzkvrmwsyyip6k";
+      rev = "a7b5edc1872b76e6c0cc18b89fcda3aa98422961";
+      sha256 = "1k92n93bcy24fqfairqqkxd7l9adc0azggp4lp3r0rh7dsglnsf0";
     };
   };
 
@@ -3721,12 +3721,12 @@ let
 
   vim-jade = buildVimPluginFrom2Nix {
     pname = "vim-jade";
-    version = "2019-05-07";
+    version = "2019-09-23";
     src = fetchFromGitHub {
       owner = "digitaltoad";
       repo = "vim-jade";
-      rev = "efed0c8680d22bd16b9dc7e08f5373269b67c45f";
-      sha256 = "0dq0mmx2bg304b24cp337lr29r0f1wkvhq9i3z54bw3x3pbw5hal";
+      rev = "ea39cd942cf3194230cf72bfb838901a5344d3b3";
+      sha256 = "07141jkfnaia4ydc6qcg0bc06w720l2lzl7bm4bsjwswqrzmhfam";
     };
   };
 
@@ -4261,12 +4261,12 @@ let
 
   vim-polyglot = buildVimPluginFrom2Nix {
     pname = "vim-polyglot";
-    version = "2019-09-12";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "sheerun";
       repo = "vim-polyglot";
-      rev = "4f3df59be709bf0d5c5c67dc804fde49abdc2700";
-      sha256 = "0rknm6bj75ax2a81bkw96nqakn2gb1mjfb6lgg8kwvcjzddfvmb9";
+      rev = "f95026252c5a31242903a98c741887696dfbb11f";
+      sha256 = "0lzzlrwcic3vbn6rk3vcakwg6fl6nkvhamxcind6jx43pr1ylwwv";
     };
   };
 
@@ -4690,23 +4690,23 @@ let
 
   vim-terraform = buildVimPluginFrom2Nix {
     pname = "vim-terraform";
-    version = "2019-09-15";
+    version = "2019-09-26";
     src = fetchFromGitHub {
       owner = "hashivim";
       repo = "vim-terraform";
-      rev = "81dd8ea296660a51618cefed62462ddff56f22fa";
-      sha256 = "1im4klyfgz5ab98ygc0jw1h9gnylab8zvzm4pk2rga2zbz9ymkxj";
+      rev = "a9925ccef810d01e3a21295d4dba97532d14f2ee";
+      sha256 = "0il49wyidin463x16b2lcf7cb5rqidqqwv56vxv9znrg6wqn94wp";
     };
   };
 
   vim-test = buildVimPluginFrom2Nix {
     pname = "vim-test";
-    version = "2019-09-01";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "janko-m";
       repo = "vim-test";
-      rev = "5aaa872eb7519909b87abb2b0f13600aa2210771";
-      sha256 = "0wvjf3fhhj9qm5p7azk2dgi3aa1qw16pzm5nkl2jr5gn2cmlphd8";
+      rev = "3c2cc7c87882c4034f4ce0a9b71980b127a680a3";
+      sha256 = "0jac3cf7cidwqf0lvlkdkg6m2r0xng3xyzsh0iyn1dw6qg3wzi2y";
     };
   };
 
@@ -4855,12 +4855,12 @@ let
 
   vim-visual-multi = buildVimPluginFrom2Nix {
     pname = "vim-visual-multi";
-    version = "2019-09-12";
+    version = "2019-09-26";
     src = fetchFromGitHub {
       owner = "mg979";
       repo = "vim-visual-multi";
-      rev = "6ff6e336ac3df959c8d0462be277b4fff8661421";
-      sha256 = "1drp53cvbflr6x94vy0f57fg9nb3kxlaxvrc5w71id4mv0pr7bb2";
+      rev = "56104bd06a30c08bf0c0dd69a98d5cb516a3025c";
+      sha256 = "1fjn4cdw99y78c8gway1pg9sbqgyr0jbbr6snh8awlnmgwa3yrg7";
     };
   };
 
@@ -5009,12 +5009,12 @@ let
 
   vimtex = buildVimPluginFrom2Nix {
     pname = "vimtex";
-    version = "2019-09-20";
+    version = "2019-09-27";
     src = fetchFromGitHub {
       owner = "lervag";
       repo = "vimtex";
-      rev = "ece9f454ac2f590629ebbbbe4b0bb23deafdcb04";
-      sha256 = "05h1hya3c4k9z1x2k13k1a1zpq8lf7nr8ggg548mmayh0cv5qvqs";
+      rev = "53ba80c91162aa84ccbfd12dbd30435d869c1391";
+      sha256 = "1lmy7fzpyga9mk26xhcq5j2i3nmzzrnbgnpi0darfg8334bzw251";
     };
   };
 
@@ -5209,12 +5209,12 @@ let
 
   zig-vim = buildVimPluginFrom2Nix {
     pname = "zig-vim";
-    version = "2019-09-19";
+    version = "2019-09-26";
     src = fetchFromGitHub {
       owner = "zig-lang";
       repo = "zig.vim";
-      rev = "29d9358a825c56a31f6438ea93eb09f091998f0d";
-      sha256 = "1rah0fm3qxv3jjb0ma2pn5kvbg2fwg4p5ycgm6vjbq95j73f5aq1";
+      rev = "08ba9f9354698c3ab85bf84b8390ce909d3bc221";
+      sha256 = "1m44hm7jgv1v5z88mi5ha0p1lrffxx2h0p25vxq12zd2x834vghf";
     };
   };
 
diff --git a/pkgs/os-specific/linux/fuse/default.nix b/pkgs/os-specific/linux/fuse/default.nix
index f48e528b486..4a1fe56c5e1 100644
--- a/pkgs/os-specific/linux/fuse/default.nix
+++ b/pkgs/os-specific/linux/fuse/default.nix
@@ -11,7 +11,7 @@ in {
   };
 
   fuse_3 = mkFuse {
-    version = "3.6.2";
-    sha256Hash = "1cxx94q6zqns1iw5d4g3ll8f78swqxl6h25bpxmqkqsj6c91pzkl";
+    version = "3.7.0";
+    sha256Hash = "0l22gv5h84j5m7khs7l82jw834i8wf7hcgagpsn9y02x7ymmiha2";
   };
 }
diff --git a/pkgs/os-specific/linux/kernel/linux-testing-bcachefs.nix b/pkgs/os-specific/linux/kernel/linux-testing-bcachefs.nix
index 0b2ed76a4b4..38c0ad10ae5 100644
--- a/pkgs/os-specific/linux/kernel/linux-testing-bcachefs.nix
+++ b/pkgs/os-specific/linux/kernel/linux-testing-bcachefs.nix
@@ -1,13 +1,13 @@
 { stdenv, buildPackages, fetchgit, fetchpatch, perl, buildLinux, ... } @ args:
 
 buildLinux (args // {
-  version = "5.1.2019.08.21";
-  modDirVersion = "5.1.0";
+  version = "5.2.2019.09.24";
+  modDirVersion = "5.2.0";
 
   src = fetchgit {
     url = "https://evilpiepirate.org/git/bcachefs.git";
-    rev = "ece184f718c2b678738bc2c42906e90eeb8ba7dc";
-    sha256 = "08cbisgcww8fklpxwqkm2c8ddz0mm7v11ycp7ch0kalwdv2f81lr";
+    rev = "5a3a4087af27aa10da5f23cb174a439946153584";
+    sha256 = "1yn40n2iyflbfv1z8l86nixv8wlybg7abz49nq5k6hmf7r9z56mk";
   };
 
   extraConfig = "BCACHEFS_FS m";
diff --git a/pkgs/os-specific/linux/nvidia-x11/default.nix b/pkgs/os-specific/linux/nvidia-x11/default.nix
index c41ce5994a1..e3affca1220 100644
--- a/pkgs/os-specific/linux/nvidia-x11/default.nix
+++ b/pkgs/os-specific/linux/nvidia-x11/default.nix
@@ -39,18 +39,6 @@ rec {
     sha256_64bit = "0h0jcckqpd63vaj95lvdgj2sbbn9y1ri1xx7r2snxfx0plhwz46n";
     settingsSha256 = "1w5nkxs7a40mq0qf97nhfazdqhfn1bvr54v50s8p0ggixb6vdm3l";
     persistencedSha256 = "02v76202qcnh8hvg4y9wmk9swdlv7z39ppfd1c850nlv158vn5nf";
-
-    patches = [
-      (fetchurl {
-        url = "https://git.archlinux.org/svntogit/packages.git/plain/trunk/kernel-4.16.patch?h=2ad07241ea525a6b6b555b6cb96a97634a4b2cb0";
-        sha256 = "11b3dp0na496rn13v5q4k66bf61174800g36rcwj42r0xj9cfak2";
-      })
-
-      (fetchurl {
-        url = "https://git.archlinux.org/svntogit/packages.git/plain/trunk/kernel-5.1.patch?h=42d50ef8d6048608d18bdf2c296dd335260c5a1a";
-        sha256 = "03v46ym2bcckg9q2xrilkg21hfiwypr6gl4jmly2q3m4yza9ja6r";
-      })
-    ];
   };
 
   legacy_340 = generic {
diff --git a/pkgs/os-specific/linux/zfs/build-fixes-0.8.patch b/pkgs/os-specific/linux/zfs/build-fixes-0.8.patch
deleted file mode 100644
index ff2c6e2e150..00000000000
--- a/pkgs/os-specific/linux/zfs/build-fixes-0.8.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From b323e7a7ebb2327943851fa3fd139399eb24d3dd Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= <joerg@thalheim.io>
-Date: Mon, 13 Aug 2018 22:58:21 +0200
-Subject: [PATCH] build fixes needed for nixos
-
----
- module/Makefile.in | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/module/Makefile.in b/module/Makefile.in
-index 935bd2663..afb08df81 100644
---- a/module/Makefile.in
-+++ b/module/Makefile.in
-@@ -44,15 +44,15 @@ clean:
- modules_install:
- 	@# Install the kernel modules
- 	$(MAKE) -C @LINUX_OBJ@ M=`pwd` $@ \
--		INSTALL_MOD_PATH=$(DESTDIR)$(INSTALL_MOD_PATH) \
-+		INSTALL_MOD_PATH=@prefix@/$(INSTALL_MOD_PATH) \
- 		INSTALL_MOD_DIR=$(INSTALL_MOD_DIR) \
- 		KERNELRELEASE=@LINUX_VERSION@
- 	@# Remove extraneous build products when packaging
--	kmoddir=$(DESTDIR)$(INSTALL_MOD_PATH)/lib/modules/@LINUX_VERSION@; \
--	if [ -n "$(DESTDIR)" ]; then \
-+	kmoddir=@prefix@$(INSTALL_MOD_PATH)/lib/modules/@LINUX_VERSION@; \
-+	if [ -n "@prefix@" ]; then \
- 		find $$kmoddir -name 'modules.*' | xargs $(RM); \
- 	fi
--	sysmap=$(DESTDIR)$(INSTALL_MOD_PATH)/boot/System.map-@LINUX_VERSION@; \
-+	sysmap=@prefix@$(INSTALL_MOD_PATH)/boot/System.map-@LINUX_VERSION@; \
- 	if [ -f $$sysmap ]; then \
- 		depmod -ae -F $$sysmap @LINUX_VERSION@; \
- 	fi
--- 
-2.19.2
-
diff --git a/pkgs/os-specific/linux/zfs/default.nix b/pkgs/os-specific/linux/zfs/default.nix
index f704a8a2a6c..899e5f05509 100644
--- a/pkgs/os-specific/linux/zfs/default.nix
+++ b/pkgs/os-specific/linux/zfs/default.nix
@@ -19,7 +19,7 @@ let
 
   common = { version
     , sha256
-    , extraPatches
+    , extraPatches ? []
     , rev ? "zfs-${version}"
     , isUnstable ? false
     , incompatibleKernelVersion ? null }:
@@ -103,6 +103,7 @@ let
       installFlags = [
         "sysconfdir=\${out}/etc"
         "DEFAULT_INITCONF_DIR=\${out}/default"
+        "INSTALL_MOD_PATH=\${out}"
       ];
 
       postInstall = optionalString buildKernel ''
@@ -157,10 +158,6 @@ in {
     version = "0.8.2";
 
     sha256 = "0miax0h2wg4b2kn8n93804faajy2n1sh25knyy2hg3k77nlr4pni";
-
-    extraPatches = [
-      ./build-fixes-0.8.patch
-    ];
   };
 
   zfsUnstable = common {
@@ -172,9 +169,5 @@ in {
 
     sha256 = "0miax0h2wg4b2kn8n93804faajy2n1sh25knyy2hg3k77nlr4pni";
     isUnstable = true;
-
-    extraPatches = [
-      ./build-fixes-0.8.patch
-    ];
   };
 }
diff --git a/pkgs/servers/clickhouse/default.nix b/pkgs/servers/clickhouse/default.nix
index ab2d44577c0..6418bd917f1 100644
--- a/pkgs/servers/clickhouse/default.nix
+++ b/pkgs/servers/clickhouse/default.nix
@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   pname = "clickhouse";
-  version = "19.13.1.11";
+  version = "19.13.5.44";
 
   src = fetchFromGitHub {
     owner  = "yandex";
     repo   = "ClickHouse";
     rev    = "v${version}-stable";
-    sha256 = "1j9jhgl2z84id5z6rbvyal7aha5v3m8pd393cmcsf1bf0fiz8qmc";
+    sha256 = "1h0jjpa1wrms5vcgx1vf8fmkc7jjrql1r70dvwr0nw8f7rfyi1l6";
   };
 
   nativeBuildInputs = [ cmake libtool ninja ];
diff --git a/pkgs/servers/http/openresty/default.nix b/pkgs/servers/http/openresty/default.nix
index 3990c5de818..53773302963 100644
--- a/pkgs/servers/http/openresty/default.nix
+++ b/pkgs/servers/http/openresty/default.nix
@@ -5,11 +5,11 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   pname = "openresty";
-  version = "1.15.8.1";
+  version = "1.15.8.2";
 
   src = fetchurl {
     url = "https://openresty.org/download/openresty-${version}.tar.gz";
-    sha256 = "0hh8aygyzxgb0cyafqin70nbi87jpnjvxbf00dljssbpl66278c9";
+    sha256 = "05jxrb8hv758nm38jil8n63q1nhrz3d249bsrwc7maa7sn24wss3";
   };
 
   buildInputs = [ openssl zlib pcre libxml2 libxslt gd geoip postgresql ];
diff --git a/pkgs/servers/mail/postfix/default.nix b/pkgs/servers/mail/postfix/default.nix
index b299d212a18..8b6a46b9657 100644
--- a/pkgs/servers/mail/postfix/default.nix
+++ b/pkgs/servers/mail/postfix/default.nix
@@ -26,11 +26,11 @@ in stdenv.mkDerivation rec {
 
   pname = "postfix";
 
-  version = "3.4.6";
+  version = "3.4.7";
 
   src = fetchurl {
     url = "ftp://ftp.cs.uu.nl/mirror/postfix/postfix-release/official/${pname}-${version}.tar.gz";
-    sha256 = "09p3vg2xlh6iq45gp6zanbp1728fc31r7zz71r131vh20ssajx6n";
+    sha256 = "0rzr0n1gljhmxidsslbr9505xcv0hm8jahkp4dm87a1v3l956cpy";
   };
 
   nativeBuildInputs = [ makeWrapper m4 ];
diff --git a/pkgs/servers/memcached/default.nix b/pkgs/servers/memcached/default.nix
index a9873261d78..bd1acd36278 100644
--- a/pkgs/servers/memcached/default.nix
+++ b/pkgs/servers/memcached/default.nix
@@ -1,12 +1,12 @@
 {stdenv, fetchurl, cyrus_sasl, libevent}:
 
 stdenv.mkDerivation rec {
-  version = "1.5.16";
+  version = "1.5.18";
   pname = "memcached";
 
   src = fetchurl {
     url = "https://memcached.org/files/${pname}-${version}.tar.gz";
-    sha256 = "0nnccb697jhdn5gqrh3phibzs6xr4nf4ryv7nmyv5vf11n4jr8j5";
+    sha256 = "127g4l0ilb376dpgz6qby24vc72ban35c938dzmp1nh6bdqddgcy";
   };
 
   configureFlags = [
diff --git a/pkgs/servers/monitoring/nagios/default.nix b/pkgs/servers/monitoring/nagios/default.nix
index 475d79a090a..693e67ee6dd 100644
--- a/pkgs/servers/monitoring/nagios/default.nix
+++ b/pkgs/servers/monitoring/nagios/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "nagios";
-  version = "4.4.4";
+  version = "4.4.5";
 
   src = fetchurl {
     url = "mirror://sourceforge/nagios/nagios-4.x/${pname}-${version}/${pname}-${version}.tar.gz";
-    sha256 = "0nkbv8lzpiknddiq0466dlpp3hw8lqmaidk8931hp4664cdsaw57";
+    sha256 = "079rgi3dqdg6h511c96hrch62rxsap9p4x37hm2nj672zb9f4sdz";
   };
 
   patches = [ ./nagios.patch ];
diff --git a/pkgs/servers/monitoring/prometheus/wireguard-exporter.nix b/pkgs/servers/monitoring/prometheus/wireguard-exporter.nix
index 9b0d91747ad..249a3f8a089 100644
--- a/pkgs/servers/monitoring/prometheus/wireguard-exporter.nix
+++ b/pkgs/servers/monitoring/prometheus/wireguard-exporter.nix
@@ -2,13 +2,13 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "wireguard-exporter";
-  version = "3.1.0";
+  version = "3.1.1";
 
   src = fetchFromGitHub {
     owner = "MindFlavor";
     repo = "prometheus_wireguard_exporter";
     rev = version;
-    sha256 = "0hl82cg6cijk3xf35cgi4v14gmxk3fj4c3z1x5hrs2i0j1i26ilw";
+    sha256 = "1cc36bngpjq8138f98d2dl0imgisiph7xmw1i7csmjs03b4pnfcx";
   };
 
   cargoSha256 = "1ndb33bi08j40b4jkj4q7d3k0cw5fscz2gc2cc3134nbs2r7jamk";
diff --git a/pkgs/servers/sql/monetdb/default.nix b/pkgs/servers/sql/monetdb/default.nix
index 245bd811c1a..34ebebbbcc1 100644
--- a/pkgs/servers/sql/monetdb/default.nix
+++ b/pkgs/servers/sql/monetdb/default.nix
@@ -3,7 +3,7 @@
 }:
 
 let
-  version = "11.33.3";
+  version = "11.33.11";
 in stdenv.mkDerivation {
 
   pname = "monetdb";
@@ -11,7 +11,7 @@ in stdenv.mkDerivation {
 
   src = fetchurl {
     url = "https://dev.monetdb.org/downloads/sources/archive/MonetDB-${version}.tar.bz2";
-    sha256 = "0k0xcm3b5qq2arjfn8f1h020sjkk97qfynsimn848bnl01vscqh8";
+    sha256 = "1fzgf1hplwlki6l6yvrk8an9y4jj40xzl4m5x1d8vi3xr526bzc9";
   };
 
   postPatch = ''
diff --git a/pkgs/servers/sql/pgbouncer/default.nix b/pkgs/servers/sql/pgbouncer/default.nix
index 30be61a805a..76b35a345b5 100644
--- a/pkgs/servers/sql/pgbouncer/default.nix
+++ b/pkgs/servers/sql/pgbouncer/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "pgbouncer";
-  version = "1.10.0";
+  version = "1.11.0";
 
   src = fetchurl {
     url = "https://pgbouncer.github.io/downloads/files/${version}/${pname}-${version}.tar.gz";
-    sha256 = "1m8vsxyna5grs5p0vnxf3fxxnkk9aqjf3qmr2bbkpkhlzr11986q";
+    sha256 = "0w3y53kwnkcm9fmf28zbjvqk6ivfic5f2k3nflvca1i8iaj2z044";
   };
 
   buildInputs = [ libevent openssl c-ares pkg-config ];
diff --git a/pkgs/shells/powershell/default.nix b/pkgs/shells/powershell/default.nix
index a7fe9634fee..b999070a49e 100644
--- a/pkgs/shells/powershell/default.nix
+++ b/pkgs/shells/powershell/default.nix
@@ -4,8 +4,8 @@
 let platformString = if stdenv.isDarwin then "osx"
                      else if stdenv.isLinux then "linux"
                      else throw "unsupported platform";
-    platformSha = if stdenv.isDarwin then "005ax54l7752lhrvlpsyn2yywr4zh58psc7sc1qv9p86d414pmkq"
-                     else if stdenv.isLinux then "1b3n6d2xgvqybmh61smyr415sfaymiilixlvs04yxm6ajsbnsm82"
+    platformSha = if stdenv.isDarwin then "0jb2xm79m3m14zk7v730ai1zvxcb5a13jbkkya0qy7332k6gn6bl"
+                     else if stdenv.isLinux then "0s0jvc9ha6fw8qy7f5n0v6zf043rawsjdlm5wvqxq1q2idz7xcw1"
                      else throw "unsupported platform";
     platformLdLibraryPath = if stdenv.isDarwin then "DYLD_FALLBACK_LIBRARY_PATH"
                      else if stdenv.isLinux then "LD_LIBRARY_PATH"
@@ -15,7 +15,7 @@ let platformString = if stdenv.isDarwin then "osx"
 in
 stdenv.mkDerivation rec {
   pname = "powershell";
-  version = "6.2.2";
+  version = "6.2.3";
 
   src = fetchzip {
     url = "https://github.com/PowerShell/PowerShell/releases/download/v${version}/powershell-${version}-${platformString}-x64.tar.gz";
diff --git a/pkgs/tools/X11/nx-libs/default.nix b/pkgs/tools/X11/nx-libs/default.nix
index c2bcfe788e6..77aada9f83f 100644
--- a/pkgs/tools/X11/nx-libs/default.nix
+++ b/pkgs/tools/X11/nx-libs/default.nix
@@ -2,12 +2,12 @@
   libpng, libtool, libxml2, pkgconfig, which, xorg }:
 stdenv.mkDerivation rec {
   pname = "nx-libs";
-  version = "3.5.99.21";
+  version = "3.5.99.22";
   src = fetchFromGitHub {
     owner = "ArcticaProject";
     repo = "nx-libs";
     rev = version;
-    sha256 = "10xid8mhhid5mrap5jb51k9fm63cm03ss4k4sfymc8zsn0wrqnr9";
+    sha256 = "0ipq93s2knv2xbb919d777mrc7v4k9l5bk0d4x6ji1bgispfa7jl";
   };
 
   nativeBuildInputs = [ autoconf automake libtool pkgconfig which
diff --git a/pkgs/tools/backup/dar/default.nix b/pkgs/tools/backup/dar/default.nix
index 352f320dadf..f48bfbd3d6a 100644
--- a/pkgs/tools/backup/dar/default.nix
+++ b/pkgs/tools/backup/dar/default.nix
@@ -3,12 +3,12 @@
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
-  version = "2.6.5";
+  version = "2.6.6";
   pname = "dar";
 
   src = fetchurl {
     url = "mirror://sourceforge/dar/${pname}-${version}.tar.gz";
-    sha256 = "1x2zr5nw3qq1vmbs4bva6mx1cx0180dri5i2971ynzcxybn75znd";
+    sha256 = "1pqdcb9dkjlf8wzpsnx4gcv9nhrm60glv4xadxnknnqlvzs6vips";
   };
 
   buildInputs = [ zlib bzip2 openssl lzo libgcrypt gpgme xz ]
diff --git a/pkgs/tools/filesystems/bcachefs-tools/default.nix b/pkgs/tools/filesystems/bcachefs-tools/default.nix
index 98dab6278b0..68783b94716 100644
--- a/pkgs/tools/filesystems/bcachefs-tools/default.nix
+++ b/pkgs/tools/filesystems/bcachefs-tools/default.nix
@@ -3,12 +3,12 @@
 
 stdenv.mkDerivation {
   pname = "bcachefs-tools";
-  version = "2019-08-21";
+  version = "2019-09-25";
 
   src = fetchgit {
     url = "https://evilpiepirate.org/git/bcachefs-tools.git";
-    rev = "72a408f84846fe702b8db4f158b678ee20bbf835";
-    sha256 = "0y5700afv1x1i3wnp3g71i3zhyhkwmx79j0irxr63fmg47n0ys1i";
+    rev = "db39aa3e1b528db3b9d731c3b054f27411e1e1a9";
+    sha256 = "19x7n51yr30dd9rrvji3xk3rij5xd8b86qiym9alpkbbyrz7h956";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/tools/filesystems/mergerfs/default.nix b/pkgs/tools/filesystems/mergerfs/default.nix
index 43c7c167b5e..4a3e860d358 100644
--- a/pkgs/tools/filesystems/mergerfs/default.nix
+++ b/pkgs/tools/filesystems/mergerfs/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "mergerfs";
-  version = "2.28.1";
+  version = "2.28.2";
 
   src = fetchFromGitHub {
     owner = "trapexit";
     repo = pname;
     rev = version;
-    sha256 = "18yc80ccpqf785gah5xw6jg5524wfra8bf3pcjr7idzdz4ca7nvf";
+    sha256 = "14h32acx2fcbyjf1f80vb86q845zwcjszd99a307ybdfhlv18r2m";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/tools/misc/crudini/default.nix b/pkgs/tools/misc/crudini/default.nix
index f5291d0789e..f63cd0d32c9 100644
--- a/pkgs/tools/misc/crudini/default.nix
+++ b/pkgs/tools/misc/crudini/default.nix
@@ -1,47 +1,53 @@
-{ stdenv, fetchFromGitHub, python2Packages, help2man }:
+{ stdenv, fetchFromGitHub, python2Packages, help2man, installShellFiles }:
 
-python2Packages.buildPythonApplication rec {
+let
+  # py3 is supposedly working in version 0.9.3 but the tests fail so stick to py2
+  pypkgs = python2Packages;
+
+in
+pypkgs.buildPythonApplication rec {
   pname = "crudini";
-  version = "0.9";
+  version = "0.9.3";
 
   src = fetchFromGitHub {
     owner  = "pixelb";
     repo   = "crudini";
     rev    = version;
-    sha256 = "0x9z9lsygripj88gadag398pc9zky23m16wmh8vbgw7ld1nhkiav";
+    sha256 = "0298hvg0fpk0m0bjpwryj3icksbckwqqsr9w1ain55wf5s0v24k3";
   };
 
-  nativeBuildInputs = [ help2man ];
-  propagatedBuildInputs = with python2Packages; [ iniparse ];
-
-  doCheck = true;
+  nativeBuildInputs = [ help2man installShellFiles ];
 
-  prePatch = ''
-    # make runs the unpatched version in src so we need to patch them in addition to tests
-    patchShebangs .
-  '';
+  propagatedBuildInputs = with pypkgs; [ iniparse ];
 
-  postBuild = ''
-    make all
+  postPatch = ''
+    substituteInPlace crudini-help \
+      --replace ./crudini $out/bin/crudini
+    substituteInPlace tests/test.sh \
+      --replace ..: $out/bin:
   '';
 
   postInstall = ''
-    mkdir -p $out/share/{man/man1,doc/crudini}
+    # this just creates the man page
+    make all
 
-    cp README EXAMPLES $out/share/doc/crudini/
-    for f in *.1 ; do
-      gzip -c $f > $out/share/man/man1/$(basename $f).gz
-    done
+    install -Dm444 -t $out/share/doc/${pname} README EXAMPLES
+    installManPage *.1
   '';
 
   checkPhase = ''
+    runHook preCheck
+
     pushd tests >/dev/null
-    ./test.sh
+    bash ./test.sh
+    popd >/dev/null
+
+    runHook postCheck
   '';
 
   meta = with stdenv.lib; {
     description = "A utility for manipulating ini files ";
-    homepage = http://www.pixelbeat.org/programs/crudini/;
+    homepage = "https://www.pixelbeat.org/programs/crudini/";
     license = licenses.gpl2;
     maintainers = with maintainers; [ peterhoeg ];
   };
diff --git a/pkgs/tools/misc/fpp/default.nix b/pkgs/tools/misc/fpp/default.nix
index ac731bcdbe8..7f036cb1f90 100644
--- a/pkgs/tools/misc/fpp/default.nix
+++ b/pkgs/tools/misc/fpp/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "fpp";
-  version = "0.8.2";
+  version = "0.9.2";
 
   src = fetchFromGitHub {
     owner = "facebook";
     repo = "PathPicker";
     rev = version;
-    sha256 = "00916xx4scd4xr9zxqkyhilczi27f2qm5y042592wr79ddix4n9v";
+    sha256 = "08p2xlz045fqyb0aj9pwwf2s5nb4b02i8zj81732q59yx5c6lrlv";
   };
 
   postPatch = ''
diff --git a/pkgs/tools/misc/parallel/default.nix b/pkgs/tools/misc/parallel/default.nix
index 06ae22c86ff..46ff72a678a 100644
--- a/pkgs/tools/misc/parallel/default.nix
+++ b/pkgs/tools/misc/parallel/default.nix
@@ -1,11 +1,11 @@
 { fetchurl, stdenv, perl, makeWrapper, procps }:
 
 stdenv.mkDerivation rec {
-  name = "parallel-20190722";
+  name = "parallel-20190922";
 
   src = fetchurl {
     url = "mirror://gnu/parallel/${name}.tar.bz2";
-    sha256 = "19xwdkmia2dw2hry9sbaq0ln79qy9dsqx11hq2s9dcyvhhqqdl0f";
+    sha256 = "0qrw34rpp8g5knb2nhs8z1hz9i42nxjn6i12m4rblm0anhnfwbr8";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/tools/misc/plantuml/default.nix b/pkgs/tools/misc/plantuml/default.nix
index eb2881b29f7..2ff042d8cbb 100644
--- a/pkgs/tools/misc/plantuml/default.nix
+++ b/pkgs/tools/misc/plantuml/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, makeWrapper, jre, graphviz }:
 
 stdenv.mkDerivation rec {
-  version = "1.2019.8";
+  version = "1.2019.11";
   pname = "plantuml";
 
   src = fetchurl {
     url = "mirror://sourceforge/project/plantuml/${version}/plantuml.${version}.jar";
-    sha256 = "0kbyjsy8zp3325syg9g91rfgy2dzkffdj2ji82b5h9zy3rkrz08p";
+    sha256 = "0k9l4d3rf5g5vwx6kd170ija872j3fafkn50fkd3ddzjqdd0v9lm";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/tools/misc/profile-sync-daemon/default.nix b/pkgs/tools/misc/profile-sync-daemon/default.nix
index 989a2d3f22b..c1496e0dbc9 100644
--- a/pkgs/tools/misc/profile-sync-daemon/default.nix
+++ b/pkgs/tools/misc/profile-sync-daemon/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, utillinux}:
 
 stdenv.mkDerivation rec {
-  version = "6.34";
+  version = "6.35";
   pname = "profile-sync-daemon";
 
   src = fetchurl {
     url = "https://github.com/graysky2/profile-sync-daemon/archive/v${version}.tar.gz";
-    sha256 = "0v6yzgfwv3mhf1q2fp6abrvr15p9b1c1gahj3mdh5b4bfcsg3n5a";
+    sha256 = "0hd3cjhf9nv4q5gvc8lbh5c82095lll7mxll1mj5hkzmnijzsf0v";
   };
 
   installPhase = ''
diff --git a/pkgs/tools/misc/rmlint/default.nix b/pkgs/tools/misc/rmlint/default.nix
index 7b7fa9ce705..408660bf3d9 100644
--- a/pkgs/tools/misc/rmlint/default.nix
+++ b/pkgs/tools/misc/rmlint/default.nix
@@ -5,13 +5,13 @@
 with stdenv.lib;
 stdenv.mkDerivation rec {
   pname = "rmlint";
-  version = "2.8.0";
+  version = "2.9.0";
 
   src = fetchFromGitHub {
     owner = "sahib";
     repo = "rmlint";
     rev = "v${version}";
-    sha256 = "1gc7gbnh0qg1kl151cv1ld87vhpm1v3pnkn7prhscdcc21jrg8nz";
+    sha256 = "1b5cziam14h80xrfb285fmfrzz2rligxcpsq1xsig14xf4l2875i";
   };
 
   CFLAGS="-I${stdenv.lib.getDev utillinux}/include";
diff --git a/pkgs/tools/misc/skim/default.nix b/pkgs/tools/misc/skim/default.nix
index 5072bfb6934..55e6e5424d7 100644
--- a/pkgs/tools/misc/skim/default.nix
+++ b/pkgs/tools/misc/skim/default.nix
@@ -2,18 +2,18 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "skim";
-  version = "0.6.8";
+  version = "0.6.9";
 
   src = fetchFromGitHub {
     owner = "lotabout";
     repo = pname;
     rev = "v${version}";
-    sha256 = "00sx1pyj0a9hkv9b8g3iykkw303vnqziddp2600nvfr8x8pd01gi";
+    sha256 = "1ygnjrljar4caybh8lqfjif4vhb33aam80ffnzgqxz6s6g85ifrb";
   };
 
   outputs = [ "out" "vim" ];
 
-  cargoSha256 = "1kqawnyddv4pjyiaizw3ydqk6hl4ng6xfw9ixy58rb1vk591kq8w";
+  cargoSha256 = "1vcxcyhhqncjii0pad775x10j1kp62y82q1mii65jclr1karml3p";
 
   patchPhase = ''
     sed -i -e "s|expand('<sfile>:h:h')|'$out'|" plugin/skim.vim
diff --git a/pkgs/tools/misc/youtube-dl/default.nix b/pkgs/tools/misc/youtube-dl/default.nix
index 98449f8f554..9ef2156af8f 100644
--- a/pkgs/tools/misc/youtube-dl/default.nix
+++ b/pkgs/tools/misc/youtube-dl/default.nix
@@ -18,11 +18,11 @@ buildPythonPackage rec {
   # The websites youtube-dl deals with are a very moving target. That means that
   # downloads break constantly. Because of that, updates should always be backported
   # to the latest stable release.
-  version = "2019.09.12.1";
+  version = "2019.09.28";
 
   src = fetchurl {
     url = "https://yt-dl.org/downloads/${version}/${pname}-${version}.tar.gz";
-    sha256 = "0h7v81kcxcpy82wq9b1aiz2zg6hg7rnlcfmzd13j6k8yhr7ah9yf";
+    sha256 = "0nrk0bk6lksnmng8lwhcpkc57iibzjjamlqz8rxjpsw6dnzxz82h";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/tools/networking/boringtun/default.nix b/pkgs/tools/networking/boringtun/default.nix
index 05e9ba1282e..dfb13f2168b 100644
--- a/pkgs/tools/networking/boringtun/default.nix
+++ b/pkgs/tools/networking/boringtun/default.nix
@@ -2,25 +2,17 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "boringtun";
-  # "boringtun" is still undergoing review for security concerns.
-  # The GitHub page does not show any release yet,
-  # use 20190407 as version number to indicate that it is an unstable version.
-  version = "20190407";
+  version = "0.2.0";
 
   src = fetchFromGitHub {
     owner = "cloudflare";
     repo = pname;
-    rev = "b040eb4fd1591b1d5ceb07c6cbb0856553f50adc";
-    sha256 = "04i53dvxld2a0xzr0gfl895rcwfvisj1rfs7rl0444gml8s8xyb3";
+    rev = "v${version}";
+    sha256 = "1mijy51hd8c4as9g4ivpfxismc9m5m3nhibfvclh3wrlcmp1ha9c";
   };
 
   cargoSha256 = "1gvmshwg9b486933vfgkg2r8nn6w6dyz42hqjy74p785fcg0v5hs";
 
-  # To prevent configuration phase error that is caused by
-  # lacking a new line in file ".cargo/config",
-  # we append a new line to the end of file.
-  preConfigure = "echo '' >> .cargo/config";
-
   buildInputs = stdenv.lib.optional stdenv.isDarwin darwin.apple_sdk.frameworks.Security;
 
   # Testing this project requires sudo, Docker and network access, etc.
@@ -30,7 +22,7 @@ rustPlatform.buildRustPackage rec {
     description = "Userspace WireGuard® implementation in Rust";
     homepage = https://github.com/cloudflare/boringtun;
     license = licenses.bsd3;
-    maintainers = with maintainers; [ xrelkd ];
+    maintainers = with maintainers; [ xrelkd marsam ];
     platforms = platforms.linux ++ platforms.darwin;
   };
 }
diff --git a/pkgs/tools/networking/nbd/default.nix b/pkgs/tools/networking/nbd/default.nix
index f9df781715a..9c443696eda 100644
--- a/pkgs/tools/networking/nbd/default.nix
+++ b/pkgs/tools/networking/nbd/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl, pkgconfig, glib, which }:
 
 stdenv.mkDerivation rec {
-  name = "nbd-3.19";
+  name = "nbd-3.20";
 
   src = fetchurl {
     url = "mirror://sourceforge/nbd/${name}.tar.xz";
-    sha256 = "1446rdg490fxd8mg5gvrf4nddbw1w7lf2daxy9cpc19yy4968iml";
+    sha256 = "1kfnyx52nna2mnw264njk1dl2zc8m78sz031yp65mbmpi99v7qg0";
   };
 
   buildInputs = [ glib ]
diff --git a/pkgs/tools/networking/shadowsocks-rust/default.nix b/pkgs/tools/networking/shadowsocks-rust/default.nix
index 668d55d8927..2416ef23c8a 100644
--- a/pkgs/tools/networking/shadowsocks-rust/default.nix
+++ b/pkgs/tools/networking/shadowsocks-rust/default.nix
@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "shadowsocks-rust";
-  version = "1.7.0";
+  version = "1.7.2";
 
   src = fetchFromGitHub {
     rev = "v${version}";
     owner = "shadowsocks";
     repo = pname;
-    sha256 = "0mqjm54mp6c9mfdl3gf01v9vm2rjll8fw63n6j4qgv01y4hrsm4f";
+    sha256 = "0w7ysha46ml3j1i1knvll4pmqg291z8a2ypcy650m61dhrvkh2ng";
   };
 
-  cargoSha256 = "19wx19sbal2q5ndniv6vllayjjy5fzi8fw7fn1d23jb9l91ak7ab";
+  cargoSha256 = "18nlvqa9ha4vs9xb60hivhgcsqr69zsigfmqyig48slvwgqkbwda";
 
   buildInputs = [ openssl libsodium ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ Security ];
diff --git a/pkgs/tools/security/nwipe/default.nix b/pkgs/tools/security/nwipe/default.nix
index caaa5eba86a..62d7fb3b34a 100644
--- a/pkgs/tools/security/nwipe/default.nix
+++ b/pkgs/tools/security/nwipe/default.nix
@@ -1,13 +1,13 @@
 { stdenv, fetchFromGitHub, ncurses, parted, automake, autoconf, pkgconfig }:
 
 stdenv.mkDerivation rec {
-  version = "0.25";
+  version = "0.26";
   pname = "nwipe";
   src = fetchFromGitHub {
     owner = "martijnvanbrummelen";
     repo = "nwipe";
     rev = "v${version}";
-    sha256 = "1hx041arw82k814g9r8dqsfi736mj5nlzp2zpi8n2qfqfc1q8nir";
+    sha256 = "072gg7hafq4vncpgm62yswshg6qgbi9mg2hl0p22c7if908p4vaa";
   };
   nativeBuildInputs = [ automake autoconf pkgconfig ];
   buildInputs = [ ncurses parted ];
diff --git a/pkgs/tools/security/pass/clip-wayland-support.patch b/pkgs/tools/security/pass/clip-wayland-support.patch
new file mode 100644
index 00000000000..7b8d2eb010d
--- /dev/null
+++ b/pkgs/tools/security/pass/clip-wayland-support.patch
@@ -0,0 +1,113 @@
+From b0b784b1a57c0b06936e6f5d6560712b4b810cd3 Mon Sep 17 00:00:00 2001
+From: Brett Cornwall <brett@i--b.com>
+Date: Wed, 27 Feb 2019 00:08:33 -0700
+Subject: clip: Add support for wl-clipboard
+
+Edited to properly apply with
+`set-correct-program-name-for-sleep.patch`.
+
+---
+ README                |  4 +++-
+ man/pass.1            |  5 +++++
+ src/password-store.sh | 26 +++++++++++++++++++++-----
+ 3 files changed, 29 insertions(+), 6 deletions(-)
+
+diff --git a/README b/README
+index 6b59965..1a46242 100644
+--- a/README
++++ b/README
+@@ -19,8 +19,10 @@ Depends on:
+   http://www.gnupg.org/
+ - git
+   http://www.git-scm.com/
+-- xclip
++- xclip (for X11 environments)
+   http://sourceforge.net/projects/xclip/
++- wl-clipboard (for wlroots Wayland-based environments)
++  https://github.com/bugaevc/wl-clipboard
+ - tree >= 1.7.0
+   http://mama.indstate.edu/users/ice/tree/
+ - GNU getopt
+diff --git a/man/pass.1 b/man/pass.1
+index 01a3fbe..a555dcb 100644
+--- a/man/pass.1
++++ b/man/pass.1
+@@ -99,6 +99,8 @@ Decrypt and print a password named \fIpass-name\fP. If \fI--clip\fP or \fI-c\fP
+ is specified, do not print the password but instead copy the first (or otherwise specified)
+ line to the clipboard using
+ .BR xclip (1)
++or
++.BR wl-clipboard(1)
+ and then restore the clipboard after 45 (or \fIPASSWORD_STORE_CLIP_TIME\fP) seconds. If \fI--qrcode\fP
+ or \fI-q\fP is specified, do not print the password but instead display a QR code using
+ .BR qrencode (1)
+@@ -132,6 +134,8 @@ in generating passwords can be changed with the \fIPASSWORD_STORE_CHARACTER_SET\
+ If \fI--clip\fP or \fI-c\fP is specified, do not print the password but instead copy
+ it to the clipboard using
+ .BR xclip (1)
++or
++.BR wl-clipboard(1)
+ and then restore the clipboard after 45 (or \fIPASSWORD_STORE_CLIP_TIME\fP) seconds. If \fI--qrcode\fP
+ or \fI-q\fP is specified, do not print the password but instead display a QR code using
+ .BR qrencode (1)
+@@ -466,6 +470,7 @@ The location of the text editor used by \fBedit\fP.
+ .BR tr (1),
+ .BR git (1),
+ .BR xclip (1),
++.BR wl-clipboard (1),
+ .BR qrencode (1).
+ 
+ .SH AUTHOR
+diff --git a/src/password-store.sh b/src/password-store.sh
+index d89d455..284eabf 100755
+--- a/src/password-store.sh
++++ b/src/password-store.sh
+@@ -152,16 +152,32 @@ check_sneaky_paths() {
+ #
+ 
+ clip() {
++	if [[ -n $WAYLAND_DISPLAY ]]; then
++		local copy_cmd=( wl-copy )
++		local paste_cmd=( wl-paste -n )
++		if [[ $X_SELECTION == primary ]]; then
++			copy_cmd+=( --primary )
++			paste_cmd+=( --primary )
++		fi
++		local display_name="$WAYLAND_DISPLAY"
++	elif [[ -n $DISPLAY ]]; then
++		local copy_cmd=( xclip -selection "$X_SELECTION" )
++		local paste_cmd=( xclip -o -selection "$X_SELECTION" )
++		local display_name="$DISPLAY"
++	else
++		die "Error: No X11 or Wayland display detected"
++	fi
++	local sleep_argv0="password store sleep on display $display_name"
++
+ 	# This base64 business is because bash cannot store binary data in a shell
+ 	# variable. Specifically, it cannot store nulls nor (non-trivally) store
+ 	# trailing new lines.
+-	local sleep_argv0="password store sleep on display $DISPLAY"
+ 	pkill -P $(pgrep -f "^$sleep_argv0") 2>/dev/null && sleep 0.5
+-	local before="$(xclip -o -selection "$X_SELECTION" 2>/dev/null | $BASE64)"
+-	echo -n "$1" | xclip -selection "$X_SELECTION" || die "Error: Could not copy data to the clipboard"
++	local before="$("${paste_cmd[@]}" 2>/dev/null | $BASE64)"
++	echo -n "$1" | "${copy_cmd[@]}" || die "Error: Could not copy data to the clipboard"
+ 	(
+ 		( exec -a "$sleep_argv0" bash <(echo trap 'kill %1' TERM\; sleep "$CLIP_TIME & wait") )
+-		local now="$(xclip -o -selection "$X_SELECTION" | $BASE64)"
++		local now="$("${paste_cmd[@]}" | $BASE64)"
+ 		[[ $now != $(echo -n "$1" | $BASE64) ]] && before="$now"
+ 
+ 		# It might be nice to programatically check to see if klipper exists,
+@@ -173,7 +189,7 @@ clip() {
+ 		# so we axe it here:
+ 		qdbus org.kde.klipper /klipper org.kde.klipper.klipper.clearClipboardHistory &>/dev/null
+ 
+-		echo "$before" | $BASE64 -d | xclip -selection "$X_SELECTION"
++		echo "$before" | $BASE64 -d | "${copy_cmd[@]}"
+ 	) >/dev/null 2>&1 & disown
+ 	echo "Copied $2 to clipboard. Will clear in $CLIP_TIME seconds."
+ }
+-- 
+cgit v1.2.1-28-gf32c
+
diff --git a/pkgs/tools/security/pass/default.nix b/pkgs/tools/security/pass/default.nix
index aeb838c0576..5d0e94bc803 100644
--- a/pkgs/tools/security/pass/default.nix
+++ b/pkgs/tools/security/pass/default.nix
@@ -4,6 +4,7 @@
 
 , xclip ? null, xdotool ? null, dmenu ? null
 , x11Support ? !stdenv.isDarwin
+, waylandSupport ? false, wl-clipboard ? null
 
 # For backwards-compatibility
 , tombPluginSupport ? false
@@ -15,6 +16,8 @@ assert x11Support -> xclip != null
                   && xdotool != null
                   && dmenu != null;
 
+assert waylandSupport -> wl-clipboard != null;
+
 let
   passExtensions = import ./extensions { inherit pkgs; };
 
@@ -37,8 +40,11 @@ let
       sha256 = "1x53k5dn3cdmvy8m4fqdld4hji5n676ksl0ql4armkmsds26av1b";
     };
 
-    patches = [ ./set-correct-program-name-for-sleep.patch
-              ] ++ stdenv.lib.optional stdenv.isDarwin ./no-darwin-getopt.patch;
+    patches = [ ./set-correct-program-name-for-sleep.patch ]
+      ++ stdenv.lib.optional stdenv.isDarwin ./no-darwin-getopt.patch
+      # TODO (@Ma27) this patch adds support for wl-clipboard and can be removed during the next
+      # version bump.
+      ++ stdenv.lib.optional waylandSupport ./clip-wayland-support.patch;
 
     nativeBuildInputs = [ makeWrapper ];
 
@@ -67,7 +73,8 @@ let
       qrencode
       procps
     ] ++ optional stdenv.isDarwin openssl
-      ++ ifEnable x11Support [ dmenu xclip xdotool ]);
+      ++ ifEnable x11Support [ dmenu xclip xdotool ]
+      ++ optional waylandSupport wl-clipboard);
 
     postFixup = ''
       # Link extensions env
diff --git a/pkgs/tools/security/pdfcrack/default.nix b/pkgs/tools/security/pdfcrack/default.nix
index c235c98b971..bf8f014bcfd 100644
--- a/pkgs/tools/security/pdfcrack/default.nix
+++ b/pkgs/tools/security/pdfcrack/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "pdfcrack";
-  version = "0.17";
+  version = "0.18";
 
   src = fetchurl {
     url = "mirror://sourceforge/pdfcrack/pdfcrack/pdfcrack-${version}.tar.gz";
-    sha256 = "15hfxwr9yfzkx842p0jjdjnjarny6qc5fwcpy2f6lnq047pb26sn";
+    sha256 = "035s3jzrs3ci0i53x04dzpqp9225c4s52cd722d6zqra5b2sw8w2";
   };
 
   installPhase = ''
diff --git a/pkgs/tools/system/logrotate/default.nix b/pkgs/tools/system/logrotate/default.nix
index cee092f755f..9fd6c4ea81a 100644
--- a/pkgs/tools/system/logrotate/default.nix
+++ b/pkgs/tools/system/logrotate/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   pname = "logrotate";
-  version = "3.15.0";
+  version = "3.15.1";
 
   src = fetchFromGitHub {
     owner = "logrotate";
     repo = "logrotate";
     rev = version;
-    sha256 = "094wv4d3gv5dmw55d0xij06lgcg5q9bmq49hipc2jhp4vdsj4xr5";
+    sha256 = "0l92zarygp34qnw3p5rcwqsvgz7zmmhi7lgh00vj2jb9zkjbldc0";
   };
 
   # Logrotate wants to access the 'mail' program; to be done.
diff --git a/pkgs/tools/virtualization/amazon-ecs-cli/default.nix b/pkgs/tools/virtualization/amazon-ecs-cli/default.nix
index e7c391806aa..306bd0574c9 100644
--- a/pkgs/tools/virtualization/amazon-ecs-cli/default.nix
+++ b/pkgs/tools/virtualization/amazon-ecs-cli/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "amazon-ecs-cli";
-  version = "1.15.1";
+  version = "1.16.0";
 
   src = fetchurl {
     url = "https://s3.amazonaws.com/amazon-ecs-cli/ecs-cli-linux-amd64-v${version}";
-    sha256 = "0p0z12b6z00sxzjfsvb37czgczrsi61klr5azan0f8wf32x6wc28";
+    sha256 = "0mj0y2hrl7yp8mfjgi68gvbravgwp5v58hhcclr49mdjnr4v6i9x";
   };
 
   dontUnpack = true;
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 8c7533b356a..0a27f73a16c 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -891,6 +891,10 @@ in
 
   pass = callPackage ../tools/security/pass { };
 
+  pass-wayland = callPackage ../tools/security/pass {
+    waylandSupport = true;
+  };
+
   passExtensions = recurseIntoAttrs pass.extensions;
 
   asc-key-to-qr-code-gif = callPackage ../tools/security/asc-key-to-qr-code-gif { };
@@ -11876,6 +11880,8 @@ in
 
   liburing = callPackage ../development/libraries/liburing { };
 
+  librseq = callPackage ../development/libraries/librseq { };
+
   libseccomp = callPackage ../development/libraries/libseccomp { };
 
   libsecret = callPackage ../development/libraries/libsecret { };
@@ -20745,7 +20751,7 @@ in
   syncthing-tray = callPackage ../applications/misc/syncthing-tray { };
 
   syncthingtray = libsForQt5.callPackage ../applications/misc/syncthingtray { };
-  syncthingtray-minumal = libsForQt5.callPackage ../applications/misc/syncthingtray {
+  syncthingtray-minimal = libsForQt5.callPackage ../applications/misc/syncthingtray {
     webviewSupport = false;
     jsSupport = false;
     kioPluginSupport = false;
@@ -22488,6 +22494,8 @@ in
 
   synthv1 = callPackage ../applications/audio/synthv1 { };
 
+  system-syzygy = callPackage ../games/system-syzygy { };
+
   t4kcommon = callPackage ../games/t4kcommon { };
 
   tcl2048 = callPackage ../games/tcl2048 { };
@@ -22931,6 +22939,8 @@ in
 
   kallisto = callPackage ../applications/science/biology/kallisto { };
 
+  macse = callPackage ../applications/science/biology/macse { };
+
   migrate = callPackage ../applications/science/biology/migrate { };
 
   mirtk = callPackage ../development/libraries/science/biology/mirtk { };
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 143619aeb14..d08bb33f34e 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3836,13 +3836,6 @@ in {
 
   msgpack-numpy = callPackage ../development/python-modules/msgpack-numpy {};
 
-  msgpack-python = self.msgpack.overridePythonAttrs {
-    pname = "msgpack-python";
-    postPatch = ''
-      substituteInPlace setup.py --replace "TRANSITIONAL = False" "TRANSITIONAL = True"
-    '';
-  };
-
   msrplib = callPackage ../development/python-modules/msrplib { };
 
   multipledispatch = callPackage ../development/python-modules/multipledispatch { };