Merge staging-next-22.05 into staging-22.05

maintainers/maintainer-list.nix

@@ -8976,6 +8976,16 @@
     githubId = 818502;
     name = "Nathan Yong";
   };
+  natsukium = {
+    email = "nixpkgs@natsukium.com";
+    github = "natsukium";
+    githubId = 25083790;
+    name = "Tomoya Otabi";
+    keys = [{
+      longkeyid = "ed25519/0x9EA45A31DB994C53";
+      fingerprint = "3D14 6004 004C F882 D519  6CD4 9EA4 5A31 DB99 4C53";
+    }];
+  };
   natto1784 = {
     email = "natto@weirdnatto.in";
     github = "natto1784";

nixos/modules/services/games/minecraft-server.nix

@@ -22,6 +22,15 @@ let
   '' + concatStringsSep "\n" (mapAttrsToList
     (n: v: "${n}=${cfgToString v}") cfg.serverProperties));
 
+  stopScript = pkgs.writeShellScript "minecraft-server-stop" ''
+    echo stop > ${config.systemd.sockets.minecraft-server.socketConfig.ListenFIFO}
+
+    # Wait for the PID of the minecraft server to disappear before
+    # returning, so systemd doesn't attempt to SIGKILL it.
+    while kill -0 "$1" 2> /dev/null; do
+      sleep 1s
+    done
+  '';
 
   # To be able to open the firewall, we need to read out port values in the
   # server properties, but fall back to the defaults when those don't exist.
@@ -172,16 +181,35 @@ in {
     };
     users.groups.minecraft = {};
 
+    systemd.sockets.minecraft-server = {
+      bindsTo = [ "minecraft-server.service" ];
+      socketConfig = {
+        ListenFIFO = "/run/minecraft-server.stdin";
+        SocketMode = "0660";
+        SocketUser = "minecraft";
+        SocketGroup = "minecraft";
+        RemoveOnStop = true;
+        FlushPending = true;
+      };
+    };
+
     systemd.services.minecraft-server = {
       description   = "Minecraft Server Service";
       wantedBy      = [ "multi-user.target" ];
-      after         = [ "network.target" ];
+      requires      = [ "minecraft-server.socket" ];
+      after         = [ "network.target" "minecraft-server.socket" ];
 
       serviceConfig = {
         ExecStart = "${cfg.package}/bin/minecraft-server ${cfg.jvmOpts}";
+        ExecStop = "${stopScript} $MAINPID";
         Restart = "always";
         User = "minecraft";
         WorkingDirectory = cfg.dataDir;
+
+        StandardInput = "socket";
+        StandardOutput = "journal";
+        StandardError = "journal";
+
         # Hardening
         CapabilityBoundingSet = [ "" ];
         DeviceAllow = [ "" ];

nixos/modules/services/web-apps/jitsi-meet.nix

@@ -253,9 +253,20 @@ in
         '';
       };
     };
-    systemd.services.prosody.serviceConfig = mkIf cfg.prosody.enable {
-      EnvironmentFile = [ "/var/lib/jitsi-meet/secrets-env" ];
-      SupplementaryGroups = [ "jitsi-meet" ];
+    systemd.services.prosody = mkIf cfg.prosody.enable {
+      preStart = let
+        videobridgeSecret = if cfg.videobridge.passwordFile != null then cfg.videobridge.passwordFile else "/var/lib/jitsi-meet/videobridge-secret";
+      in ''
+        ${config.services.prosody.package}/bin/prosodyctl register focus auth.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jicofo-user-secret)"
+        ${config.services.prosody.package}/bin/prosodyctl register jvb auth.${cfg.hostName} "$(cat ${videobridgeSecret})"
+        ${config.services.prosody.package}/bin/prosodyctl mod_roster_command subscribe focus.${cfg.hostName} focus@auth.${cfg.hostName}
+        ${config.services.prosody.package}/bin/prosodyctl register jibri auth.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jibri-auth-secret)"
+        ${config.services.prosody.package}/bin/prosodyctl register recorder recorder.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jibri-recorder-secret)"
+      '';
+      serviceConfig = {
+        EnvironmentFile = [ "/var/lib/jitsi-meet/secrets-env" ];
+        SupplementaryGroups = [ "jitsi-meet" ];
+      };
     };
 
     users.groups.jitsi-meet = {};
@@ -266,14 +277,12 @@ in
     systemd.services.jitsi-meet-init-secrets = {
       wantedBy = [ "multi-user.target" ];
       before = [ "jicofo.service" "jitsi-videobridge2.service" ] ++ (optional cfg.prosody.enable "prosody.service");
-      path = [ config.services.prosody.package ];
       serviceConfig = {
         Type = "oneshot";
       };
 
       script = let
         secrets = [ "jicofo-component-secret" "jicofo-user-secret" "jibri-auth-secret" "jibri-recorder-secret" ] ++ (optional (cfg.videobridge.passwordFile == null) "videobridge-secret");
-        videobridgeSecret = if cfg.videobridge.passwordFile != null then cfg.videobridge.passwordFile else "/var/lib/jitsi-meet/videobridge-secret";
       in
       ''
         cd /var/lib/jitsi-meet
@@ -291,12 +300,6 @@ in
         chmod 640 secrets-env
       ''
       + optionalString cfg.prosody.enable ''
-        prosodyctl register focus auth.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jicofo-user-secret)"
-        prosodyctl register jvb auth.${cfg.hostName} "$(cat ${videobridgeSecret})"
-        prosodyctl mod_roster_command subscribe focus.${cfg.hostName} focus@auth.${cfg.hostName}
-        prosodyctl register jibri auth.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jibri-auth-secret)"
-        prosodyctl register recorder recorder.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jibri-recorder-secret)"
-
         # generate self-signed certificates
         if [ ! -f /var/lib/jitsi-meet.crt ]; then
           ${getBin pkgs.openssl}/bin/openssl req \

nixos/tests/jitsi-meet.nix

@@ -33,9 +33,6 @@ import ./make-test-python.nix ({ pkgs, ... }: {
     server.wait_for_unit("nginx.service")
     server.wait_for_unit("prosody.service")
 
-    server.wait_until_succeeds(
-        "journalctl -b -u jitsi-videobridge2 -o cat | grep -q 'Performed a successful health check'"
-    )
     server.wait_until_succeeds(
         "journalctl -b -u prosody -o cat | grep -q 'Authenticated as focus@auth.server'"
     )

nixos/tests/minecraft-server.nix

@@ -33,5 +33,6 @@ in import ./make-test-python.nix ({ pkgs, ... }: {
     assert "${seed}" in server.succeed(
         "mcrcon -H localhost -P ${toString rcon-port} -p '${rcon-pass}' -c 'seed'"
     )
+    server.succeed("systemctl stop minecraft-server")
   '';
 })

pkgs/applications/networking/remote/rustdesk/cargo.patch

@@ -1,26 +1,24 @@
 diff --git a/Cargo.lock b/Cargo.lock
-index c3e139e..b77d8bd 100644
+index fb17c7e..ef157e5 100644
 --- a/Cargo.lock
 +++ b/Cargo.lock
-@@ -1761,11 +1761,11 @@ dependencies = [
- 
+@@ -2332,10 +2332,10 @@ dependencies = [
  [[package]]
  name = "magnum-opus"
--version = "0.3.4-2"
--source = "git+https://github.com/open-trade/magnum-opus#ad0836164abf4a4df69009b1ee08eabe3a13b33f"
-+version = "0.4.0"
+ version = "0.4.0"
+-source = "git+https://github.com/open-trade/magnum-opus#3c3d0b86ae95c84930bebffe4bcb03b3bd83342b"
 +source = "git+https://github.com/TheRadioGuy/magnum-opus#171e1d021004626f7444d1e39b98f50bc3cb2604"
  dependencies = [
-- "bindgen 0.59.1",
+- "bindgen",
 - "target_build_utils",
 + "libc",
 + "opusic-sys",
  ]
  
  [[package]]
-@@ -2188,6 +2188,16 @@ version = "0.1.4"
+@@ -2796,6 +2796,16 @@ version = "0.1.5"
  source = "registry+https://github.com/rust-lang/crates.io-index"
- checksum = "28988d872ab76095a6e6ac88d99b54fd267702734fd7ffe610ca27f533ddb95a"
+ checksum = "ff011a302c396a5197692431fc1948019154afc178baf7d8e37367442a4601cf"
  
 +[[package]]
 +name = "opusic-sys"
@@ -33,18 +31,18 @@ index c3e139e..b77d8bd 100644
 +]
 +
  [[package]]
- name = "parity-tokio-ipc"
- version = "0.7.2"
+ name = "os_str_bytes"
+ version = "6.0.0"
 diff --git a/Cargo.toml b/Cargo.toml
-index 75504a0..43e1624 100644
+index 1b715bd..960e8da 100644
 --- a/Cargo.toml
 +++ b/Cargo.toml
-@@ -32,7 +32,7 @@ libc = "0.2"
+@@ -35,7 +35,7 @@ libc = "0.2"
  parity-tokio-ipc = { git = "https://github.com/open-trade/parity-tokio-ipc" }
- flexi_logger = "0.17"
+ flexi_logger = { version = "0.22", features = ["async", "use_chrono_for_offset"] }
  runas = "0.2"
 -magnum-opus = { git = "https://github.com/open-trade/magnum-opus" }
 +magnum-opus = { git = "https://github.com/TheRadioGuy/magnum-opus" }
  dasp = { version = "0.11", features = ["signal", "interpolate-linear", "interpolate"], optional = true }
- rubato = { version = "0.8", optional = true }
+ rubato = { version = "0.12", optional = true }
  samplerate = { version = "0.2", optional = true }

pkgs/applications/networking/remote/rustdesk/default.nix

@@ -24,20 +24,21 @@
 , libsciter
 , llvmPackages
 , wrapGAppsHook
+, writeText
 }:
 
 rustPlatform.buildRustPackage rec {
   pname = "rustdesk";
-  version = "1.1.8";
+  version = "1.1.9";
 
   src = fetchFromGitHub {
     owner = "rustdesk";
     repo = "rustdesk";
-    rev = "0325500ebf331b66220cec6e9078afb83b0e98a7";
-    sha256 = "sha256-xglyyoiAjJx3y8+A2OYHZffjqjDkcTjIluPA/J42VVg=";
+    rev = version;
+    sha256 = "sha256-IlrfqwNyaSHE9Ct0mn7MUxEg7p1Ku34eOMYelEAYFW8=";
   };
 
-  cargoSha256 = "sha256-4MQKa54f3X7IHGd29H6RY7v2toeHvTHInIpgXjdotjw=";
+  cargoSha256 = "sha256-1OMWEk+DerltF7kwdo4d04rbgIFLHBRq3vZaL7jtrdE=";
 
   LIBCLANG_PATH="${llvmPackages.libclang.lib}/lib";
 
@@ -51,10 +52,29 @@ rustPlatform.buildRustPackage rec {
   # properly.
   postUnpack = let
     vcpkg_target = "x64-linux";
+
+    updates_vcpkg_file = writeText "update_vcpkg_rustdesk"
+    ''
+    Package : libyuv
+    Architecture : ${vcpkg_target}
+    Version : 1.0
+    Status : is installed
+
+    Package : libvpx
+    Architecture : ${vcpkg_target}
+    Version : 1.0
+    Status : is installed
+    '';
   in ''
     export VCPKG_ROOT="$TMP/vcpkg";
 
+    mkdir -p $VCPKG_ROOT/.vcpkg-root
     mkdir -p $VCPKG_ROOT/installed/${vcpkg_target}/lib
+    mkdir -p $VCPKG_ROOT/installed/vcpkg/updates
+    ln -s ${updates_vcpkg_file} $VCPKG_ROOT/installed/vcpkg/status
+    mkdir -p $VCPKG_ROOT/installed/vcpkg/info
+    touch $VCPKG_ROOT/installed/vcpkg/info/libyuv_1.0_${vcpkg_target}.list
+    touch $VCPKG_ROOT/installed/vcpkg/info/libvpx_1.0_${vcpkg_target}.list
 
     ln -s ${libvpx.out}/lib/* $VCPKG_ROOT/installed/${vcpkg_target}/lib/
     ln -s ${libyuv.out}/lib/* $VCPKG_ROOT/installed/${vcpkg_target}/lib/

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

@@ -0,0 +1,25 @@
+{ lib, stdenv, fetchFromGitHub, boost, cmake, libcifpp, zlib, }:
+
+stdenv.mkDerivation rec {
+  pname = "dssp";
+  version = "4.0.5";
+
+  src = fetchFromGitHub {
+    owner = "PDB-REDO";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1x35rdcm4fch66pjbmy73lv0gdb6g9y3v023a66512a6nzsqjsir";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ boost libcifpp zlib ];
+
+  meta = with lib; {
+    description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein";
+    homepage = "https://github.com/PDB-REDO/dssp";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+}

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

@@ -0,0 +1,27 @@
+{ lib, stdenv, fetchurl }:
+
+stdenv.mkDerivation rec {
+  pname = "mafft";
+  version = "7.490";
+
+  src = fetchurl {
+    url = "https://mafft.cbrc.jp/alignment/software/mafft-${version}-with-extensions-src.tgz";
+    sha256 = "0hb5jzcqdnjn3micm5z301lrnyvmn9pnnnxjz4h2wa4yicyz7vnn";
+  };
+
+  preBuild = ''
+    cd ./core
+    make clean
+  '';
+
+  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "PREFIX=$(out)" ];
+
+  meta = with lib;
+    {
+      description = "Multiple alignment program for amino acid or nucleotide sequences";
+      homepage = "https://mafft.cbrc.jp/alignment/software/";
+      license = licenses.bsd3;
+      maintainers = with maintainers; [ natsukium ];
+      platforms = platforms.unix;
+    };
+}

pkgs/development/libraries/ffmpeg/generic.nix

@@ -239,6 +239,7 @@ stdenv.mkDerivation rec {
     '';
     license = licenses.gpl3;
     maintainers = with maintainers; [ ];
+    platforms = platforms.all;
     inherit branch knownVulnerabilities;
   };
 }

pkgs/development/libraries/libcifpp/default.nix

@@ -0,0 +1,25 @@
+{ lib, stdenv, fetchFromGitHub, boost, cmake, }:
+
+stdenv.mkDerivation rec {
+  pname = "libcifpp";
+  version = "4.2.0";
+
+  src = fetchFromGitHub {
+    owner = "PDB-REDO";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1hzi6fgbsmy8h8nfwkyfds9jz13nqw72h0x81jqw5516kkvar5iw";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ boost ];
+
+  meta = with lib; {
+    description = "Manipulate mmCIF and PDB files";
+    homepage = "https://github.com/PDB-REDO/libcifpp";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+}

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

@@ -2,13 +2,13 @@
 
 buildPythonPackage rec {
   pname = "pivy";
-  version = "0.6.6";
+  version = "0.6.7";
 
   src = fetchFromGitHub {
     owner = "coin3d";
     repo = "pivy";
     rev = version;
-    sha256 = "1xlynrbq22pb252r37r80b3myzap8hzhvknz4zfznfrsg9ykh8k2";
+    sha256 = "mU3QRDJd56gGDWqwcxAN3yUCkAkABP/I9gIBMH2MOXA=";
   };
 
   dontUseCmakeConfigure = true;

pkgs/development/tools/metals/default.nix

@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   pname = "metals";
-  version = "0.11.5";
+  version = "0.11.7";
 
   deps = stdenv.mkDerivation {
     name = "${pname}-deps-${version}";
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
     '';
     outputHashMode = "recursive";
     outputHashAlgo = "sha256";
-    outputHash     = "sha256-kw+8688E1b7XjEb7AqOExSVu88NqPprKaCuINWqL2wk=";
+    outputHash = "sha256-Zc/0kod3JM58WpyxwXiyQdixBHOJV7UDGg1YZtHJ3hw=";
   };
 
   nativeBuildInputs = [ makeWrapper setJavaClassPath ];
@@ -29,23 +29,8 @@ stdenv.mkDerivation rec {
   installPhase = ''
     mkdir -p $out/bin
 
-    # This variant is not targeted at any particular client, clients are
-    # expected to declare their supported features in initialization options.
     makeWrapper ${jre}/bin/java $out/bin/metals \
       --add-flags "${extraJavaOpts} -cp $CLASSPATH scala.meta.metals.Main"
-
-    # Further variants targeted at clients with featuresets pre-set.
-    makeWrapper ${jre}/bin/java $out/bin/metals-emacs \
-      --add-flags "${extraJavaOpts} -Dmetals.client=emacs -cp $CLASSPATH scala.meta.metals.Main"
-
-    makeWrapper ${jre}/bin/java $out/bin/metals-vim \
-      --add-flags "${extraJavaOpts} -Dmetals.client=coc.nvim -cp $CLASSPATH scala.meta.metals.Main"
-
-    makeWrapper ${jre}/bin/java $out/bin/metals-vim-lsc \
-      --add-flags "${extraJavaOpts} -Dmetals.client=vim-lsc -cp $CLASSPATH scala.meta.metals.Main"
-
-    makeWrapper ${jre}/bin/java $out/bin/metals-sublime \
-      --add-flags "${extraJavaOpts} -Dmetals.client=sublime -cp $CLASSPATH scala.meta.metals.Main"
   '';
 
   meta = with lib; {

pkgs/misc/jitsi-meet-prosody/default.nix

@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   pname = "jitsi-meet-prosody";
-  version = "1.0.5675";
+  version = "1.0.6260";
   src = fetchurl {
     url = "https://download.jitsi.org/stable/${pname}_${version}-1_all.deb";
-    sha256 = "FrafgJcNF3xv985JJ+xOWPtJZFeElIAaIXWdcgheru0=";
+    sha256 = "ZUfyEYAU4YEYXBoM+tEZ6SAhqlNcsmxnKw8WEv0gy7M=";
   };
 
   dontBuild = true;

pkgs/servers/atlassian/crowd.nix

@@ -3,11 +3,11 @@
 
 stdenv.mkDerivation rec {
   pname = "atlassian-crowd";
-  version = "4.4.0";
+  version = "5.0.1";
 
   src = fetchurl {
     url = "https://www.atlassian.com/software/crowd/downloads/binary/${pname}-${version}.tar.gz";
-    sha256 = "0ipfvdjs8v02y37rmihljy9lkb3ycz5hyc14mcg65ilsscsq3x91";
+    sha256 = "sha256-ccXSNuiXP0+b9WObboikqVd0nKH0Fi2gMVEF3+WAx5M=";
   };
 
   buildPhase = ''

pkgs/servers/jicofo/default.nix

@@ -2,10 +2,10 @@
 
 let
   pname = "jicofo";
-  version = "1.0-832";
+  version = "1.0-900";
   src = fetchurl {
     url = "https://download.jitsi.org/stable/${pname}_${version}-1_all.deb";
-    sha256 = "ZSzxD4RCsIkNtB4agBRZkzbJOi6ttzlc4Qw5n0t5syc=";
+    sha256 = "tAuWhu1DdasOuLIz9/Ox1n1XcFWm5qnTVr6FpdKpwbE=";
   };
 in
 stdenv.mkDerivation {

pkgs/servers/jitsi-videobridge/default.nix

@@ -2,10 +2,10 @@
 
 let
   pname = "jitsi-videobridge2";
-  version = "2.1-595-g3637fda4";
+  version = "2.2-9-g8cded16e";
   src = fetchurl {
     url = "https://download.jitsi.org/stable/${pname}_${version}-1_all.deb";
-    sha256 = "vwn9C8M3wwiIqwxAu1MDe2ra2SCQ2Hssco5J/xUFoKM=";
+    sha256 = "L9h+qYV/W2wPzycfDGC4AXpTl7wlulyt2KryA+Tb/YU=";
   };
 in
 stdenv.mkDerivation {

pkgs/servers/nextcloud/default.nix

@@ -51,10 +51,10 @@ in {
   };
 
   nextcloud24 = generic {
-    version = "24.0.2";
-    sha256 = "30d6cac1265dff221836bec46a937dcafd7e7d52ee59b939841750b514e5033d";
+    version = "24.0.3";
+    sha256 = "320c81f9b902922b4bcef3eacf858596a14347fd45bddd26dac198562d212439";
   };
 
-  # tip: get she sha with:
+  # tip: get the sha with:
   # curl 'https://download.nextcloud.com/server/releases/nextcloud-${version}.tar.bz2.sha256'
 }

pkgs/servers/web-apps/jitsi-meet/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "jitsi-meet";
-  version = "1.0.6155";
+  version = "1.0.6260";
 
   src = fetchurl {
     url = "https://download.jitsi.org/jitsi-meet/src/jitsi-meet-${version}.tar.bz2";
-    sha256 = "baCRVYe1z2uH3vSb5KbWs0y4KyQYO3JpTyoGFZIZQqo=";
+    sha256 = "Y1ELKdFdbnq20yUt4XoXmstJm8uI8EBGIFOvFWf+5Uw=";
   };
 
   dontBuild = true;

pkgs/tools/admin/awscli2/default.nix

@@ -29,13 +29,13 @@ let
 in
 with py.pkgs; buildPythonApplication rec {
   pname = "awscli2";
-  version = "2.7.9"; # N.B: if you change this, check if overrides are still up-to-date
+  version = "2.7.14"; # N.B: if you change this, check if overrides are still up-to-date
 
   src = fetchFromGitHub {
     owner = "aws";
     repo = "aws-cli";
     rev = version;
-    sha256 = "sha256-6JlBgcHpR2ZfrljS+flxaog/KZQLvPUacJGLMQNsZ5Y=";
+    sha256 = "sha256-ji/hKoYxM3wag9DXy2e/VsJZVGN5UEebWX/ctOVJ42M=";
   };
 
   propagatedBuildInputs = [
@@ -101,6 +101,6 @@ with py.pkgs; buildPythonApplication rec {
     changelog = "https://github.com/aws/aws-cli/blob/${version}/CHANGELOG.rst";
     description = "Unified tool to manage your AWS services";
     license = licenses.asl20;
-    maintainers = with maintainers; [ bhipple davegallant bryanasdev000 ];
+    maintainers = with maintainers; [ bhipple davegallant bryanasdev000 devusb ];
   };
 }

pkgs/top-level/all-packages.nix

@@ -18368,6 +18368,8 @@ with pkgs;
 
   libchop = callPackage ../development/libraries/libchop { };
 
+  libcifpp = callPackage ../development/libraries/libcifpp { };
+
   libcint = callPackage ../development/libraries/libcint { };
 
   libclc = callPackage ../development/libraries/libclc { };
@@ -32821,6 +32823,8 @@ with pkgs;
 
   diamond = callPackage ../applications/science/biology/diamond { };
 
+  dssp = callPackage ../applications/science/biology/dssp { };
+
   ecopcr = callPackage ../applications/science/biology/ecopcr { };
 
   eggnog-mapper = callPackage ../applications/science/biology/eggnog-mapper { };
@@ -32865,6 +32869,8 @@ with pkgs;
 
   MACS2 = callPackage ../applications/science/biology/MACS2 { };
 
+  mafft = callPackage ../applications/science/biology/mafft { };
+
   migrate = callPackage ../applications/science/biology/migrate { };
 
   minia = callPackage ../applications/science/biology/minia { };