NixOS
diff --git a/nixos/modules/services/development/hoogle.nix b/nixos/modules/services/development/hoogle.nix
@@ -43,6 +43,12 @@ in {
       defaultText = "pkgs.haskellPackages";
     };
 
+    home = mkOption {
+      type = types.str;
+      description = "Url for hoogle logo";
+      default = "https://hoogle.haskell.org";
+    };
+
   };
 
   config = mkIf cfg.enable {
@@ -53,7 +59,7 @@ in {
 
       serviceConfig = {
         Restart = "always";
-        ExecStart = ''${hoogleEnv}/bin/hoogle server --local -p ${toString cfg.port}'';
+        ExecStart = ''${hoogleEnv}/bin/hoogle server --local --port ${toString cfg.port} --home ${cfg.home}'';
 
         User = "nobody";
         Group = "nogroup";

diff --git a/nixos/modules/services/misc/gitlab.nix b/nixos/modules/services/misc/gitlab.nix
@@ -560,6 +560,7 @@ in {
         mkdir -p ${cfg.statePath}/tmp/sockets
         mkdir -p ${cfg.statePath}/shell
         mkdir -p ${cfg.statePath}/db
+        mkdir -p ${cfg.statePath}/uploads
 
         rm -rf ${cfg.statePath}/config ${cfg.statePath}/shell/hooks
         mkdir -p ${cfg.statePath}/config
@@ -570,6 +571,7 @@ in {
         mkdir -p ${cfg.statePath}/log
         ln -sf ${cfg.statePath}/log /run/gitlab/log
         ln -sf ${cfg.statePath}/tmp /run/gitlab/tmp
+        ln -sf ${cfg.statePath}/uploads /run/gitlab/uploads
         ln -sf $GITLAB_SHELL_CONFIG_PATH /run/gitlab/shell-config.yml
         chown -R ${cfg.user}:${cfg.group} /run/gitlab
 
@@ -584,7 +586,9 @@ in {
           ln -sf ${smtpSettings} ${cfg.statePath}/config/initializers/smtp_settings.rb
         ''}
         ln -sf ${cfg.statePath}/config /run/gitlab/config
-        rm ${cfg.statePath}/lib
+        if [ -e ${cfg.statePath}/lib ]; then
+          rm ${cfg.statePath}/lib
+        fi
         ln -sf ${pkgs.gitlab}/share/gitlab/lib ${cfg.statePath}/lib
         cp ${cfg.packages.gitlab}/share/gitlab/VERSION ${cfg.statePath}/VERSION
 
@@ -608,10 +612,11 @@ in {
             ${pkgs.sudo}/bin/sudo -u ${pgSuperUser} ${config.services.postgresql.package}/bin/createdb --owner ${cfg.databaseUsername} ${cfg.databaseName}
             touch "${cfg.statePath}/db-created"
           fi
+
+          # enable required pg_trgm extension for gitlab
+          ${pkgs.sudo}/bin/sudo -u ${pgSuperUser} psql ${cfg.databaseName} -c "CREATE EXTENSION IF NOT EXISTS pg_trgm"
         fi
 
-        # enable required pg_trgm extension for gitlab
-        ${pkgs.sudo}/bin/sudo -u ${pgSuperUser} psql ${cfg.databaseName} -c "CREATE EXTENSION IF NOT EXISTS pg_trgm"
         # Always do the db migrations just to be sure the database is up-to-date
         ${gitlab-rake}/bin/gitlab-rake db:migrate RAILS_ENV=production
 

diff --git a/nixos/modules/services/network-filesystems/beegfs.nix b/nixos/modules/services/network-filesystems/beegfs.nix
@@ -195,6 +195,17 @@ in
           };
 
           helperd = {
+            enable = mkOption {
+              type = types.bool;
+              default = true;
+              description = ''
+                Enable the BeeGFS helperd.
+                The helpered is need for logging purposes on the client.
+                Disabling <literal>helperd</literal> allows for runing the client
+                with <literal>allowUnfree = false</literal>.
+              '';
+            };
+
             extraConfig = mkOption {
               type = types.lines;
               default = "";

diff --git a/nixos/modules/system/boot/systemd.nix b/nixos/modules/system/boot/systemd.nix
@@ -546,7 +546,7 @@ in
     };
 
     services.journald.rateLimitInterval = mkOption {
-      default = "10s";
+      default = "30s";
       type = types.str;
       description = ''
         Configures the rate limiting interval that is applied to all
@@ -559,7 +559,7 @@ in
     };
 
     services.journald.rateLimitBurst = mkOption {
-      default = 100;
+      default = 1000;
       type = types.int;
       description = ''
         Configures the rate limiting burst limit (number of messages per

diff --git a/pkgs/applications/graphics/yed/default.nix b/pkgs/applications/graphics/yed/default.nix
@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   name = "yEd-${version}";
-  version = "3.17.2";
+  version = "3.18.1";
 
   src = requireFile {
     name = "${name}.zip";
     url = "https://www.yworks.com/en/products/yfiles/yed/";
-    sha256 = "0wpfvd3jqxgjk3xqkamvlg7rk0w0pmrv7srjfqns447ccc3i7qg2";
+    sha256 = "6aefd87cd925b4a4c86871a3772de243b4e520a86f82158189ae8c19a9a5ecf8";
   };
 
   nativeBuildInputs = [ unzip makeWrapper ];

diff --git a/pkgs/applications/misc/dbeaver/default.nix b/pkgs/applications/misc/dbeaver/default.nix
@@ -7,7 +7,7 @@
 
 stdenv.mkDerivation rec {
   name = "dbeaver-ce-${version}";
-  version = "5.1.3";
+  version = "5.1.4";
 
   desktopItem = makeDesktopItem {
     name = "dbeaver";
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://dbeaver.io/files/${version}/dbeaver-ce-${version}-linux.gtk.x86_64.tar.gz";
-    sha256 = "1znkr28pfpclq2gl2prllb3hwq9v9rj5xl7xarq0hsggzfg9n071";
+    sha256 = "14i7b3l89rkhqq4zgsdbvcs9pp60djv0rjbm86fpk2wi4zkrlzi5";
   };
 
   installPhase = ''

diff --git a/pkgs/applications/networking/browsers/chromium/browser.nix b/pkgs/applications/networking/browsers/chromium/browser.nix
@@ -51,6 +51,6 @@ mkChromiumDerivation (base: rec {
     license = licenses.bsd3;
     platforms = platforms.linux;
     hydraPlatforms = if channel == "stable" then ["aarch64-linux" "x86_64-linux"] else [];
-    timeout = 86400; # 24 hours
+    timeout = 172800; # 48 hours
   };
 })
diff --git a/pkgs/desktops/mate/mate-control-center/default.nix b/pkgs/desktops/mate/mate-control-center/default.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   name = "mate-control-center-${version}";
-  version = "1.20.3";
+  version = "1.21.0";
 
   src = fetchurl {
     url = "http://pub.mate-desktop.org/releases/${mate.getRelease version}/${name}.tar.xz";
-    sha256 = "0wpi8b3zz10xd5i7ir7nd737a9vl4q17rc5nh8vfrqpyrcilqzkd";
+    sha256 = "0m40jr1midh5fzk3k97sydihlqfqjvzxlgmkx8w2j30a09h7230w";
   };
 
   nativeBuildInputs = [

diff --git a/pkgs/development/haskell-modules/configuration-common.nix b/pkgs/development/haskell-modules/configuration-common.nix
@@ -972,6 +972,13 @@ self: super: {
     sha256 = "0i889zs46wn09d7iqdy99201zaqxb175cfs8jz2zi3mv4ywx3a0l";
   });
 
+  # https://github.com/simonmichael/hledger/issues/852
+  hledger-lib = appendPatch super.hledger-lib (pkgs.fetchpatch {
+    url = "https://github.com/simonmichael/hledger/commit/007b9f8caaf699852511634752a7d7c86f6adc67.patch";
+    sha256 = "1lfp29mi1qyrcr9nfjigbyric0xb9n4ann5w6sr0g5sanr4maqs2";
+    stripLen = 1;
+  });
+
   # Copy hledger man pages from data directory into the proper place. This code
   # should be moved into the cabal2nix generator.
   hledger = overrideCabal super.hledger (drv: {

diff --git a/pkgs/development/interpreters/php/default.nix b/pkgs/development/interpreters/php/default.nix
@@ -231,8 +231,8 @@ in {
   };
 
   php71 = generic {
-    version = "7.1.19";
-    sha256 = "1wvhsxzmb78pcr36ginz93iv7rcrxp3p01rb34zxa2h4wdxkxi0k";
+    version = "7.1.20";
+    sha256 = "0i8xd6p4zdg8fl6f0j430raanlshsshr3s3jlm72b0gvi1n4f6rs";
   };
 
   php72 = generic {

diff --git a/pkgs/development/libraries/jsonrpc-glib/default.nix b/pkgs/development/libraries/jsonrpc-glib/default.nix
@@ -0,0 +1,40 @@
+{ stdenv, fetchurl, meson, ninja, glib, json-glib, pkgconfig, gobjectIntrospection, vala, gtk-doc, docbook_xsl, docbook_xml_dtd_43, gnome3 }:
+let
+  version = "3.28.1";
+  pname = "jsonrpc-glib";
+in
+stdenv.mkDerivation {
+  name = "${pname}-${version}";
+
+  outputs = [ "out" "dev" "devdoc" ];
+
+  nativeBuildInputs = [ meson ninja pkgconfig gobjectIntrospection vala gtk-doc docbook_xsl docbook_xml_dtd_43 ];
+  buildInputs = [ glib json-glib ];
+
+  src = fetchurl {
+    url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
+    sha256 = "0avff2ldjvwrb8rnzlgslagdjf6x7bmdx69rsq20k6f38icw4ang";
+  };
+
+  mesonFlags = [
+    "-Denable_gtk_doc=true"
+  ];
+
+  # Tests fail non-deterministically
+  # https://gitlab.gnome.org/GNOME/jsonrpc-glib/issues/2
+  doCheck = false;
+
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = pname;
+    };
+  };
+
+  meta = with stdenv.lib; {
+    description = "A library to communicate using the JSON-RPC 2.0 specification";
+    homepage = https://gitlab.gnome.org/GNOME/jsonrpc-glib;
+    license = licenses.lgpl21Plus;
+    maintainers = gnome3.maintainers;
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/development/libraries/msgpuck/default.nix b/pkgs/development/libraries/msgpuck/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, fetchFromGitHub, cmake, pkgconfig }:
+
+stdenv.mkDerivation rec {
+  name = "msgpuck-${version}";
+  version = "2.0";
+
+  src = fetchFromGitHub {
+    owner = "rtsisyk";
+    repo = "msgpuck";
+    rev = "${version}";
+    sha256 = "0cjq86kncn3lv65vig9cqkqqv2p296ymcjjbviw0j1s85cfflps0";
+  };
+
+  outputs = [ "out" "dev" ];
+
+  nativeBuildInputs = [ cmake pkgconfig ];
+
+  meta = with stdenv.lib; {
+     description = ''A simple and efficient MsgPack binary serialization library in a self-contained header file'';
+     homepage = https://github.com/rtsisyk/msgpuck;
+     license = licenses.bsd2;
+     platforms = platforms.linux;
+     maintainers = with maintainers; [ izorkin ];
+ };
+}
diff --git a/pkgs/development/libraries/ptex/default.nix b/pkgs/development/libraries/ptex/default.nix
@@ -3,13 +3,13 @@
 stdenv.mkDerivation rec
 {
   name = "ptex-${version}";
-  version = "2.1.33";
+  version = "2.3.0";
 
   src = fetchFromGitHub {
     owner = "wdas";
     repo = "ptex";
     rev = "v${version}";
-    sha256 = "15ijjq3w7hwgm4mqah0x4jzjy3v2nnmmv28lbqzmxzcxjgh4sjkn";
+    sha256 = "0nfz0y66bmi6xckn1whi4sfd8i3ibln212fgm4img2z98b6vccyg";
   };
 
   outputs = [ "bin" "dev" "out" "lib" ];

diff --git a/pkgs/development/libraries/template-glib/default.nix b/pkgs/development/libraries/template-glib/default.nix
@@ -0,0 +1,36 @@
+{ stdenv, fetchurl, meson, ninja, pkgconfig, glib, gobjectIntrospection, flex, bison, vala, gettext, gnome3, gtk-doc, docbook_xsl, docbook_xml_dtd_43 }:
+let
+  version = "3.28.0";
+  pname = "template-glib";
+in
+stdenv.mkDerivation {
+  name = "${pname}-${version}";
+
+  outputs = [ "out" "dev" "devdoc" ];
+
+  src = fetchurl {
+    url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
+    sha256 = "18bic41f9cx8h6n5bz80z4ridb8c1h1yscicln8zsn23zmp44x3c";
+  };
+
+  buildInputs = [ meson ninja pkgconfig gettext flex bison vala glib gtk-doc docbook_xsl docbook_xml_dtd_43 ];
+  nativeBuildInputs = [ glib gobjectIntrospection ];
+
+  mesonFlags = [
+    "-Denable_gtk_doc=true"
+  ];
+
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = pname;
+    };
+  };
+
+  meta = with stdenv.lib; {
+    description = "A library for template expansion which supports calling into GObject Introspection from templates";
+    homepage = https://gitlab.gnome.org/GNOME/template-glib;
+    license = licenses.lgpl21Plus;
+    maintainers = gnome3.maintainers;
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/development/python-modules/contextvars/default.nix b/pkgs/development/python-modules/contextvars/default.nix
@@ -2,12 +2,12 @@
 
 buildPythonPackage rec {
   pname = "contextvars";
-  version = "2.2";
+  version = "2.3";
   disabled = !isPy36;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "046b385nfzkjh0wqmd268p2jkgn9fg6hz40npq7j1w3c8aqzhwvx";
+    sha256 = "09fnni8cyxm070bfv9ay030qbyk0dfds5nq77s0p38h33hp08h93";
   };
 
   propagatedBuildInputs = [ immutables ];

diff --git a/pkgs/development/python-modules/libusb1/default.nix b/pkgs/development/python-modules/libusb1/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, buildPythonPackage, fetchPypi, libusb1 }:
+{ stdenv, lib, buildPythonPackage, fetchPypi, python, libusb1 }:
 
 buildPythonPackage rec {
   pname = "libusb1";
@@ -17,6 +17,10 @@ buildPythonPackage rec {
 
   buildInputs = [ libusb1 ];
 
+  checkPhase = ''
+    ${python.interpreter} -m usb1.testUSB1
+  '';
+
   meta = with stdenv.lib; {
     homepage    = https://github.com/vpelletier/python-libusb1;
     description = "Python ctype-based wrapper around libusb1";

diff --git a/pkgs/development/python-modules/pytest-flake8/default.nix b/pkgs/development/python-modules/pytest-flake8/default.nix
@@ -2,7 +2,7 @@
 
 buildPythonPackage rec {
   pname = "pytest-flake8";
-  version = "1.0.1";
+  version = "1.0.2";
 
   # although pytest is a runtime dependency, do not add it as
   # propagatedBuildInputs in order to allow packages depend on another version
@@ -12,16 +12,13 @@ buildPythonPackage rec {
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0s5fdivrmhjf6ybr6m2qb1h8hndv2jh2ir29qv36lhy9b7sc9kg5";
+    sha256 = "c740ad6aa19e3958947d2118f70bed218caf1d2097039fb7318573a2a72f89a1";
   };
 
   checkPhase = ''
-    pytest . -k "not test_mtime_caching"
+    pytest .
   '';
 
-  # https://github.com/tholo/pytest-flake8/issues/49
-  doCheck = false;
-
   meta = {
     description = "py.test plugin for efficiently checking PEP8 compliance";
     homepage = https://github.com/tholo/pytest-flake8;

diff --git a/pkgs/development/tools/analysis/rr/default.nix b/pkgs/development/tools/analysis/rr/default.nix
@@ -51,6 +51,6 @@ stdenv.mkDerivation rec {
 
     license = "custom";
     maintainers = with stdenv.lib.maintainers; [ pierron thoughtpolice ];
-    platforms = ["x86_64-linux"];
+    platforms = stdenv.lib.platforms.x86;
   };
 }