Revert "Merge master into staging-next"

I merged master into staging-next but accidentally pushed it to master.
This should get us back to 87a19e9.

This reverts commit ac241fb, reversing
changes made to 76a4392.

lib/strings.nix

@@ -244,7 +244,7 @@ rec {
      Also note that Nix treats strings as a list of bytes and thus doesn't
      handle unicode.
 
-     Type: stringToCharacters :: string -> [string]
+     Type: stringtoCharacters :: string -> [string]
 
      Example:
        stringToCharacters ""

nixos/modules/installer/cd-dvd/iso-image.nix

@@ -569,18 +569,14 @@ in
       };
 
     fileSystems."/nix/store" =
-      { fsType = "overlay";
-        device = "overlay";
-        options = [
-          "lowerdir=/nix/.ro-store"
-          "upperdir=/nix/.rw-store/store"
-          "workdir=/nix/.rw-store/work"
-        ];
+      { fsType = "unionfs-fuse";
+        device = "unionfs";
+        options = [ "allow_other" "cow" "nonempty" "chroot=/mnt-root" "max_files=32768" "hide_meta_files" "dirs=/nix/.rw-store=rw:/nix/.ro-store=ro" ];
       };
 
-    boot.initrd.availableKernelModules = [ "squashfs" "iso9660" "uas" "overlay" ];
+    boot.initrd.availableKernelModules = [ "squashfs" "iso9660" "uas" ];
 
-    boot.initrd.kernelModules = [ "loop" "overlay" ];
+    boot.initrd.kernelModules = [ "loop" ];
 
     # Closures to be copied to the Nix store on the CD, namely the init
     # script and the top-level system configuration directory.

nixos/modules/installer/netboot/netboot.nix

@@ -50,18 +50,14 @@ with lib;
       };
 
     fileSystems."/nix/store" =
-      { fsType = "overlay";
-        device = "overlay";
-        options = [
-          "lowerdir=/nix/.ro-store"
-          "upperdir=/nix/.rw-store/store"
-          "workdir=/nix/.rw-store/work"
-        ];
+      { fsType = "unionfs-fuse";
+        device = "unionfs";
+        options = [ "allow_other" "cow" "nonempty" "chroot=/mnt-root" "max_files=32768" "hide_meta_files" "dirs=/nix/.rw-store=rw:/nix/.ro-store=ro" ];
       };
 
-    boot.initrd.availableKernelModules = [ "squashfs" "overlay" ];
+    boot.initrd.availableKernelModules = [ "squashfs" ];
 
-    boot.initrd.kernelModules = [ "loop" "overlay" ];
+    boot.initrd.kernelModules = [ "loop" ];
 
     # Closures to be copied to the Nix store, namely the init
     # script and the top-level system configuration directory.

nixos/modules/misc/ids.nix

@@ -299,7 +299,7 @@ in
       couchpotato = 267;
       gogs = 268;
       pdns-recursor = 269;
-      #kresd = 270; # switched to "knot-resolver" with dynamic ID
+      kresd = 270;
       rpc = 271;
       geoip = 272;
       fcron = 273;
@@ -600,7 +600,7 @@ in
       headphones = 266;
       couchpotato = 267;
       gogs = 268;
-      #kresd = 270; # switched to "knot-resolver" with dynamic ID
+      kresd = 270;
       #rpc = 271; # unused
       #geoip = 272; # unused
       fcron = 273;

nixos/modules/services/networking/kresd.nix

@@ -3,34 +3,12 @@
 with lib;
 
 let
-  cfg = config.services.kresd;
-
-  # Convert systemd-style address specification to kresd config line(s).
-  # On Nix level we don't attempt to precisely validate the address specifications.
-  mkListen = kind: addr: let
-    al_v4 = builtins.match "([0-9.]\+):([0-9]\+)" addr;
-    al_v6 = builtins.match "\\[(.\+)]:([0-9]\+)" addr;
-    al_portOnly = builtins.match "()([0-9]\+)" addr;
-    al = findFirst (a: a != null)
-      (throw "services.kresd.*: incorrect address specification '${addr}'")
-      [ al_v4 al_v6 al_portOnly ];
-    port = last al;
-    addrSpec = if al_portOnly == null then "'${head al}'" else "{'::', '127.0.0.1'}";
-    in # freebind is set for compatibility with earlier kresd services;
-       # it could be configurable, for example.
-      ''
-        net.listen(${addrSpec}, ${port}, { kind = '${kind}', freebind = true })
-      '';
 
-  configFile = pkgs.writeText "kresd.conf" (
-    optionalString (cfg.listenDoH != []) ''
-      modules.load('http')
-    ''
-    + concatMapStrings (mkListen "dns") cfg.listenPlain
-    + concatMapStrings (mkListen "tls") cfg.listenTLS
-    + concatMapStrings (mkListen "doh") cfg.listenDoH
-    + cfg.extraConfig
-  );
+  cfg = config.services.kresd;
+  configFile = pkgs.writeText "kresd.conf" ''
+    ${optionalString (cfg.listenDoH != []) "modules.load('http')"}
+    ${cfg.extraConfig};
+  '';
 
   package = pkgs.knot-resolver.override {
     extraFeatures = cfg.listenDoH != [];
@@ -47,7 +25,6 @@ in {
           value
       )
     )
-    (mkRemovedOptionModule [ "services" "kresd" "cacheDir" ] "Please use (bind-)mounting instead.")
   ];
 
   ###### interface
@@ -58,8 +35,8 @@ in {
       description = ''
         Whether to enable knot-resolver domain name server.
         DNSSEC validation is turned on by default.
-        You can run <literal>sudo nc -U /run/knot-resolver/control/1</literal>
-        and give commands interactively to kresd@1.service.
+        You can run <literal>sudo nc -U /run/kresd/control</literal>
+        and give commands interactively to kresd.
       '';
     };
     extraConfig = mkOption {
@@ -69,10 +46,16 @@ in {
         Extra lines to be added verbatim to the generated configuration file.
       '';
     };
+    cacheDir = mkOption {
+      type = types.path;
+      default = "/var/cache/kresd";
+      description = ''
+        Directory for caches.  They are intended to survive reboots.
+      '';
+    };
     listenPlain = mkOption {
       type = with types; listOf str;
       default = [ "[::1]:53" "127.0.0.1:53" ];
-      example = [ "53" ];
       description = ''
         What addresses and ports the server should listen on.
         For detailed syntax see ListenStream in man systemd.socket.
@@ -92,54 +75,91 @@ in {
       default = [];
       example = [ "198.51.100.1:443" "[2001:db8::1]:443" "443" ];
       description = ''
-        Addresses and ports on which kresd should provide DNS over HTTPS (see RFC 8484).
+        Addresses and ports on which kresd should provide DNS over HTTPS (see RFC 7858).
         For detailed syntax see ListenStream in man systemd.socket.
       '';
     };
-    instances = mkOption {
-      type = types.ints.unsigned;
-      default = 1;
-      description = ''
-        The number of instances to start.  They will be called kresd@{1,2,...}.service.
-        Knot Resolver uses no threads, so this is the way to scale.
-        You can dynamically start/stop them at will, so this is just system default.
-      '';
-    };
     # TODO: perhaps options for more common stuff like cache size or forwarding
   };
 
   ###### implementation
   config = mkIf cfg.enable {
-    environment.etc."knot-resolver/kresd.conf".source = configFile; # not required
+    environment.etc."kresd.conf".source = configFile; # not required
 
-    users.users.knot-resolver =
-      { isSystemUser = true;
-        group = "knot-resolver";
+    users.users.kresd =
+      { uid = config.ids.uids.kresd;
+        group = "kresd";
         description = "Knot-resolver daemon user";
       };
-    users.groups.knot-resolver.gid = null;
+    users.groups.kresd.gid = config.ids.gids.kresd;
+
+    systemd.sockets.kresd = rec {
+      wantedBy = [ "sockets.target" ];
+      before = wantedBy;
+      listenStreams = cfg.listenPlain;
+      socketConfig = {
+        ListenDatagram = listenStreams;
+        FreeBind = true;
+        FileDescriptorName = "dns";
+      };
+    };
 
-    systemd.packages = [ package ]; # the units are patched inside the package a bit
+    systemd.sockets.kresd-tls = mkIf (cfg.listenTLS != []) rec {
+      wantedBy = [ "sockets.target" ];
+      before = wantedBy;
+      partOf = [ "kresd.socket" ];
+      listenStreams = cfg.listenTLS;
+      socketConfig = {
+        FileDescriptorName = "tls";
+        FreeBind = true;
+        Service = "kresd.service";
+      };
+    };
 
-    systemd.targets.kresd = { # configure units started by default
-      wantedBy = [ "multi-user.target" ];
-      wants = [ "kres-cache-gc.service" ]
-        ++ map (i: "kresd@${toString i}.service") (range 1 cfg.instances);
+    systemd.sockets.kresd-doh = mkIf (cfg.listenDoH != []) rec {
+      wantedBy = [ "sockets.target" ];
+      before = wantedBy;
+      partOf = [ "kresd.socket" ];
+      listenStreams = cfg.listenDoH;
+      socketConfig = {
+        FileDescriptorName = "doh";
+        FreeBind = true;
+        Service = "kresd.service";
+      };
     };
-    systemd.services."kresd@".serviceConfig = {
-      ExecStart = "${package}/bin/kresd --noninteractive "
-        + "-c ${package}/lib/knot-resolver/distro-preconfig.lua -c ${configFile}";
-      # Ensure correct ownership in case UID or GID changes.
-      CacheDirectory = "knot-resolver";
-      CacheDirectoryMode = "0750";
+
+    systemd.sockets.kresd-control = rec {
+      wantedBy = [ "sockets.target" ];
+      before = wantedBy;
+      partOf = [ "kresd.socket" ];
+      listenStreams = [ "/run/kresd/control" ];
+      socketConfig = {
+        FileDescriptorName = "control";
+        Service = "kresd.service";
+        SocketMode = "0660"; # only root user/group may connect and control kresd
+      };
     };
 
-    environment.etc."tmpfiles.d/knot-resolver.conf".source =
-      "${package}/lib/tmpfiles.d/knot-resolver.conf";
+    systemd.tmpfiles.rules = [ "d '${cfg.cacheDir}' 0770 kresd kresd - -" ];
 
-    # Try cleaning up the previously default location of cache file.
-    # Note that /var/cache/* should always be safe to remove.
-    # TODO: remove later, probably between 20.09 and 21.03
-    systemd.tmpfiles.rules = [ "R /var/cache/kresd" ];
+    systemd.services.kresd = {
+      description = "Knot-resolver daemon";
+
+      serviceConfig = {
+        User = "kresd";
+        Type = "notify";
+        WorkingDirectory = cfg.cacheDir;
+        Restart = "on-failure";
+        Sockets = [ "kresd.socket" "kresd-control.socket" ]
+          ++ optional (cfg.listenTLS != []) "kresd-tls.socket";
+      };
+
+      # Trust anchor goes from dns-root-data by default.
+      script = ''
+        exec '${package}/bin/kresd' --config '${configFile}' --forks=1
+      '';
+
+      requires = [ "kresd.socket" ];
+    };
   };
 }

nixos/modules/system/boot/stage-1-init.sh

@@ -334,10 +334,8 @@ mountFS() {
 
     # Filter out x- options, which busybox doesn't do yet.
     local optionsFiltered="$(IFS=,; for i in $options; do if [ "${i:0:2}" != "x-" ]; then echo -n $i,; fi; done)"
-    # Prefix (lower|upper|work)dir with /mnt-root (overlayfs)
-    local optionsPrefixed="$( echo "$optionsFiltered" | sed -E 's#\<(lowerdir|upperdir|workdir)=#\1=/mnt-root#g' )"
 
-    echo "$device /mnt-root$mountPoint $fsType $optionsPrefixed" >> /etc/fstab
+    echo "$device /mnt-root$mountPoint $fsType $optionsFiltered" >> /etc/fstab
 
     checkFS "$device" "$fsType"
 
@@ -356,11 +354,10 @@ mountFS() {
             ;;
     esac
 
-    # Create backing directories for overlayfs
-    if [ "$fsType" = overlay ]; then
-        for i in upper work; do
-             dir="$( echo "$optionsPrefixed" | grep -o "${i}dir=[^,]*" )"
-             mkdir -m 0700 -p "${dir##*=}"
+    # Create backing directories for unionfs-fuse.
+    if [ "$fsType" = unionfs-fuse ]; then
+        for i in $(IFS=:; echo ${options##*,dirs=}); do
+            mkdir -m 0700 -p /mnt-root"${i%=*}"
         done
     fi
 

nixos/tests/lorri/default.nix

@@ -15,12 +15,12 @@ import ../make-test-python.nix {
 
     # Start the daemon and wait until it is ready
     machine.execute("lorri daemon > lorri.stdout 2> lorri.stderr &")
-    machine.wait_until_succeeds("grep --fixed-strings 'ready' lorri.stdout")
+    machine.wait_until_succeeds("grep --fixed-strings 'lorri: ready' lorri.stdout")
 
     # Ping the daemon
-    machine.succeed("lorri internal__ping shell.nix")
+    machine.execute("lorri ping_ $(readlink -f shell.nix)")
 
     # Wait for the daemon to finish the build
-    machine.wait_until_succeeds("grep --fixed-strings 'Completed' lorri.stdout")
+    machine.wait_until_succeeds("grep --fixed-strings 'OutputPaths' lorri.stdout")
   '';
 }

pkgs/applications/graphics/paraview/default.nix

@@ -1,5 +1,9 @@
-{ stdenv, fetchFromGitHub, cmake, makeWrapper, qtbase , qttools, python
-, libGLU, libGL , libXt, qtx11extras, qtxmlpatterns , mkDerivation }:
+{
+stdenv, fetchFromGitHub, cmake, makeWrapper
+,qtbase, qttools, python, libGLU, libGL
+,libXt, qtx11extras, qtxmlpatterns
+, mkDerivation
+}:
 
 mkDerivation rec {
   pname = "paraview";
@@ -49,20 +53,20 @@ mkDerivation rec {
 
   # Paraview links into the Python library, resolving symbolic links on the way,
   # so we need to put the correct sitePackages (with numpy) back on the path
-  preFixup = ''
-    wrapQtApp $out/bin/paraview \
+  postInstall = ''
+    wrapProgram $out/bin/paraview \
       --prefix PYTHONPATH "${python.pkgs.numpy}/${python.sitePackages}"
-    wrapQtApp $out/bin/pvbatch \
+    wrapProgram $out/bin/pvbatch \
       --prefix PYTHONPATH "${python.pkgs.numpy}/${python.sitePackages}"
-    wrapQtApp $out/bin/pvpython \
+    wrapProgram $out/bin/pvpython \
       --prefix PYTHONPATH "${python.pkgs.numpy}/${python.sitePackages}"
   '';
 
-  meta = with stdenv.lib; {
+  meta = {
     homepage = http://www.paraview.org/;
     description = "3D Data analysis and visualization application";
-    license = licenses.free;
-    maintainers = with maintainers; [ guibert ];
-    platforms = platforms.linux;
+    license = stdenv.lib.licenses.free;
+    maintainers = with stdenv.lib.maintainers; [guibert];
+    platforms = with stdenv.lib.platforms; linux;
   };
 }

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

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "SPAdes";
-  version = "3.14.0";
+  version = "3.13.1";
 
   src = fetchurl {
     url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz";
-    sha256 = "1ffxswd2ngkpy1d6l3lb6a9cmyy1fglbdsws00b3m1k22zaqv60q";
+    sha256 = "0giayz197lmq2108filkn9izma3i803sb3iskv9hs5snzdr9p8ld";
   };
 
   nativeBuildInputs = [ cmake ];