Merge staging-next into staging

2024-04-05 06:01:46 +00:00 · 2024-04-05 06:01:46 +00:00 · 110bd4dbee
commit 110bd4dbee
parent 2ff2fe727d 9a0c25978d
99 changed files with 4469 additions and 3314 deletions
--- a/README.md
+++ b/README.md
@ -1,9 +1,9 @@
 <p align="center">
  <a href="https://nixos.org">
    <picture>
-      <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/NixOS/nixos-homepage/master/logo/nixos-hires.png">
+      <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/NixOS/nixos-homepage/main/public/logo/nixos-hires.png">
      <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/NixOS/nixos-artwork/master/logo/nixos-white.png">
-      <img src="https://raw.githubusercontent.com/NixOS/nixos-homepage/master/logo/nixos-hires.png" width="500px" alt="NixOS logo">
+      <img src="https://raw.githubusercontent.com/NixOS/nixos-homepage/main/public/logo/nixos-hires.png" width="500px" alt="NixOS logo">
    </picture>
  </a>
 </p>
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@ -1425,6 +1425,12 @@
    githubId = 4194320;
    name = "Anton Schirg";
  };
+  aorith = {
+    email = "aomanu+nixpkgs@gmail.com";
+    github = "aorith";
+    githubId = 5411704;
+    name = "Manuel Sanchez Pinar";
+  };
  apeschar = {
    email = "albert@peschar.net";
    github = "apeschar";
--- a/nixos/modules/module-list.nix
+++ b/nixos/modules/module-list.nix
@ -1389,6 +1389,7 @@
  ./services/web-apps/rss-bridge.nix
  ./services/web-apps/selfoss.nix
  ./services/web-apps/shiori.nix
+  ./services/web-apps/silverbullet.nix
  ./services/web-apps/slskd.nix
  ./services/web-apps/snipe-it.nix
  ./services/web-apps/sogo.nix
--- a/nixos/modules/services/system/cloud-init.nix
+++ b/nixos/modules/services/system/cloud-init.nix
@ -204,7 +204,7 @@ in
      description = "Apply the settings specified in cloud-config";
      wantedBy = [ "multi-user.target" ];
      wants = [ "network-online.target" ];
-      after = [ "network-online.target" "syslog.target" "cloud-config.target" ];
+      after = [ "network-online.target" "cloud-config.target" ];

      path = path;
      serviceConfig = {
@ -220,7 +220,7 @@ in
      description = "Execute cloud user/final scripts";
      wantedBy = [ "multi-user.target" ];
      wants = [ "network-online.target" ];
-      after = [ "network-online.target" "syslog.target" "cloud-config.service" "rc-local.service" ];
+      after = [ "network-online.target" "cloud-config.service" "rc-local.service" ];
      requires = [ "cloud-config.target" ];
      path = path;
      serviceConfig = {
--- a/nixos/modules/services/web-apps/silverbullet.nix
+++ b/nixos/modules/services/web-apps/silverbullet.nix
@ -0,0 +1,123 @@
+{ config
+, pkgs
+, lib
+, ...
+}:
+let
+  cfg = config.services.silverbullet;
+  defaultUser = "silverbullet";
+  defaultGroup = defaultUser;
+  defaultSpaceDir = "/var/lib/silverbullet";
+in
+{
+  options = {
+    services.silverbullet = {
+      enable = lib.mkEnableOption (lib.mdDoc "Silverbullet, an open-source, self-hosted, offline-capable Personal Knowledge Management (PKM) web application.");
+
+      package = lib.mkPackageOptionMD pkgs "silverbullet" { };
+
+      openFirewall = lib.mkOption {
+        type = lib.types.bool;
+        default = false;
+        description = lib.mdDoc "Open port in the firewall.";
+      };
+
+      listenPort = lib.mkOption {
+        type = lib.types.int;
+        default = 3000;
+        description = lib.mdDoc "Port to listen on.";
+      };
+
+      listenAddress = lib.mkOption {
+        type = lib.types.str;
+        default = "127.0.0.1";
+        description = lib.mdDoc "Address or hostname to listen on. Defaults to 127.0.0.1.";
+      };
+
+      spaceDir = lib.mkOption {
+        type = lib.types.path;
+        default = defaultSpaceDir;
+        example = "/home/yourUser/silverbullet";
+        description = lib.mdDoc ''
+          Folder to store Silverbullet's space/workspace.
+          By default it is located at `${defaultSpaceDir}`.
+        '';
+      };
+
+      user = lib.mkOption {
+        type = lib.types.str;
+        default = defaultUser;
+        example = "yourUser";
+        description = lib.mdDoc ''
+          The user to run Silverbullet as.
+          By default, a user named `${defaultUser}` will be created whose space
+          directory is [spaceDir](#opt-services.silverbullet.spaceDir).
+        '';
+      };
+
+      group = lib.mkOption {
+        type = lib.types.str;
+        default = defaultGroup;
+        example = "yourGroup";
+        description = lib.mdDoc ''
+          The group to run Silverbullet under.
+          By default, a group named `${defaultGroup}` will be created.
+        '';
+      };
+
+      envFile = lib.mkOption {
+        type = lib.types.nullOr lib.types.path;
+        default = null;
+        example = "/etc/silverbullet.env";
+        description = lib.mdDoc ''
+          File containing extra environment variables. For example:
+
+          ```
+          SB_USER=user:password
+          SB_AUTH_TOKEN=abcdefg12345
+          ```
+        '';
+      };
+
+      extraArgs = lib.mkOption {
+        type = lib.types.listOf lib.types.str;
+        default = [ ];
+        example = [ "--db /path/to/silverbullet.db" ];
+        description = lib.mdDoc "Extra arguments passed to silverbullet.";
+      };
+    };
+  };
+
+  config = lib.mkIf cfg.enable {
+    systemd.services.silverbullet = {
+      description = "Silverbullet service";
+      after = [ "network.target" ];
+      wantedBy = [ "multi-user.target" ];
+
+      preStart = lib.mkIf (!lib.hasPrefix "/var/lib/" cfg.spaceDir) "mkdir -p '${cfg.spaceDir}'";
+      serviceConfig = {
+        Type = "simple";
+        User = "${cfg.user}";
+        Group = "${cfg.group}";
+        EnvironmentFile = lib.mkIf (cfg.envFile != null) "${cfg.envFile}";
+        StateDirectory = lib.mkIf (lib.hasPrefix "/var/lib/" cfg.spaceDir) (lib.last (lib.splitString "/" cfg.spaceDir));
+        ExecStart = "${lib.getExe cfg.package} --port ${toString cfg.listenPort} --hostname '${cfg.listenAddress}' '${cfg.spaceDir}' " + lib.concatStringsSep " " cfg.extraArgs;
+        Restart = "on-failure";
+      };
+    };
+
+    networking.firewall = lib.mkIf cfg.openFirewall {
+      allowedTCPPorts = [ cfg.listenPort ];
+    };
+
+    users.users.${defaultUser} = lib.mkIf (cfg.user == defaultUser) {
+      isSystemUser = true;
+      group = cfg.group;
+      description = "Silverbullet daemon user";
+    };
+
+    users.groups.${defaultGroup} = lib.mkIf (cfg.group == defaultGroup) { };
+  };
+
+  meta.maintainers = with lib.maintainers; [ aorith ];
+}
--- a/nixos/tests/all-tests.nix
+++ b/nixos/tests/all-tests.nix
@ -811,6 +811,7 @@ in {
  shattered-pixel-dungeon = handleTest ./shattered-pixel-dungeon.nix {};
  shiori = handleTest ./shiori.nix {};
  signal-desktop = handleTest ./signal-desktop.nix {};
+  silverbullet = handleTest ./silverbullet.nix {};
  simple = handleTest ./simple.nix {};
  sing-box = handleTest ./sing-box.nix {};
  slimserver = handleTest ./slimserver.nix {};
--- a/nixos/tests/silverbullet.nix
+++ b/nixos/tests/silverbullet.nix
@ -0,0 +1,47 @@
+import ./make-test-python.nix ({ lib, ... }: {
+  name = "silverbullet";
+  meta.maintainers = with lib.maintainers; [ aorith ];
+
+  nodes.simple = { ... }: {
+    services.silverbullet.enable = true;
+  };
+
+  nodes.configured = { pkgs, ... }: {
+    users.users.test.isNormalUser = true;
+    users.groups.test = { };
+
+    services.silverbullet = {
+      enable = true;
+      package = pkgs.silverbullet;
+      listenPort = 3001;
+      listenAddress = "localhost";
+      spaceDir = "/home/test/silverbullet";
+      user = "test";
+      group = "test";
+      envFile = pkgs.writeText "silverbullet.env" ''
+        SB_USER=user:password
+        SB_AUTH_TOKEN=test
+      '';
+      extraArgs = [ "--reindex" "--db /home/test/silverbullet/custom.db" ];
+    };
+  };
+
+  testScript = { nodes, ... }: ''
+    PORT = ${builtins.toString nodes.simple.services.silverbullet.listenPort}
+    ADDRESS = "${nodes.simple.services.silverbullet.listenAddress}"
+    SPACEDIR = "${nodes.simple.services.silverbullet.spaceDir}"
+    simple.wait_for_unit("silverbullet.service")
+    simple.wait_for_open_port(PORT)
+    simple.succeed(f"curl --max-time 5 -s -v -o /dev/null --fail http://{ADDRESS}:{PORT}/")
+    simple.succeed(f"test -d '{SPACEDIR}'")
+
+    PORT = ${builtins.toString nodes.configured.services.silverbullet.listenPort}
+    ADDRESS = "${nodes.configured.services.silverbullet.listenAddress}"
+    SPACEDIR = "${nodes.configured.services.silverbullet.spaceDir}"
+    configured.wait_for_unit("silverbullet.service")
+    configured.wait_for_open_port(PORT)
+    assert int(configured.succeed(f"curl --max-time 5 -s -o /dev/null -w '%{{http_code}}' -XPUT -d 'test' --fail http://{ADDRESS}:{PORT}/test.md -H'Authorization: Bearer test'")) == 200
+    assert int(configured.fail(f"curl --max-time 5 -s -o /dev/null -w '%{{http_code}}' -XPUT -d 'test' --fail http://{ADDRESS}:{PORT}/test.md -H'Authorization: Bearer wrong'")) == 401
+    configured.succeed(f"test -d '{SPACEDIR}'")
+  '';
+})
--- a/pkgs/applications/audio/faustPhysicalModeling/default.nix
+++ b/pkgs/applications/audio/faustPhysicalModeling/default.nix
@ -1,13 +1,13 @@
 { stdenv, lib, fetchFromGitHub, faust2jaqt, faust2lv2 }:
 stdenv.mkDerivation rec {
  pname = "faustPhysicalModeling";
-  version = "2.70.3";
+  version = "2.72.14";

  src = fetchFromGitHub {
    owner = "grame-cncm";
    repo = "faust";
    rev = version;
-    sha256 = "sha256-QkksliLu2TnJ1GoM91e+Qf3SlRv3T06WNU++S3qq3e0=";
+    sha256 = "sha256-UBMVU2oAfoAaSQXxZxV+LFq8dyb5dvy/0cCG4XywZVc=";
  };

  buildInputs = [ faust2jaqt faust2lv2 ];
--- a/pkgs/applications/audio/geonkick/default.nix
+++ b/pkgs/applications/audio/geonkick/default.nix
@ -3,13 +3,13 @@

 stdenv.mkDerivation rec {
  pname = "geonkick";
-  version = "3.3.1";
+  version = "3.4.0";

  src = fetchFromGitLab {
    owner = "Geonkick-Synthesizer";
    repo = pname;
    rev = "v${version}";
-    sha256 = "sha256-fsDoqQqZsoeQa66dxb8JC2ywUFmBf6b2J+/ixWZTzfU=";
+    sha256 = "sha256-zoEC85QYcQMF92KvLBikYw1nDoSHaedpTDDqvoAtte0=";
  };

  nativeBuildInputs = [ cmake pkg-config ];
--- a/pkgs/applications/audio/grandorgue/default.nix
+++ b/pkgs/applications/audio/grandorgue/default.nix
@ -21,14 +21,14 @@

 stdenv.mkDerivation rec {
  pname = "grandorgue";
-  version = "3.14.0";
+  version = "3.14.0-1";

  src = fetchFromGitHub {
    owner = "GrandOrgue";
    repo = pname;
    rev = version;
    fetchSubmodules = true;
-    hash = "sha256-kPz11V2yNmBe80egNLYxh/m2B1nDca3C5sGbEnrkqnw=";
+    hash = "sha256-bzGfc0kWlQSjvZsFlRERPjdLtemcZmsa6DsQGgBPoFo=";
  };

  postPatch = ''
--- a/pkgs/applications/graphics/lightburn/default.nix
+++ b/pkgs/applications/graphics/lightburn/default.nix
@ -6,7 +6,7 @@

 stdenv.mkDerivation rec {
  pname = "lightburn";
-  version = "1.5.05";
+  version = "1.5.06";

  nativeBuildInputs = [
    p7zip
@ -15,7 +15,7 @@ stdenv.mkDerivation rec {

  src = fetchurl {
    url = "https://github.com/LightBurnSoftware/deployment/releases/download/${version}/LightBurn-Linux64-v${version}.7z";
-    sha256 = "sha256-rvskm0Br+3HqPo2DW/ZUIl8n3+UJKPlmkEtQofw05x4=";
+    sha256 = "sha256-VJMfvZHqdgUQXLyBBZLEV3nyP0qzibuXLnZyBhBBg9E=";
  };

  buildInputs = [
--- a/pkgs/applications/misc/fspy/default.nix
+++ b/pkgs/applications/misc/fspy/default.nix
@ -19,6 +19,7 @@ in appimageTools.wrapType2 {
    description = "A cross platform app for quick and easy still image camera matching";
    license = licenses.gpl3;
    homepage = "https://fspy.io/";
+    knownVulnerabilities = [ "Vendors Electron 2.0 (end-of-life)" ];
    maintainers = with maintainers; [ polygon ];
    platforms = platforms.linux;
    mainProgram = "fspy";
--- a/pkgs/applications/misc/keepassxc/default.nix
+++ b/pkgs/applications/misc/keepassxc/default.nix
@ -27,6 +27,7 @@
 , LocalAuthentication

 , withKeePassBrowser ? true
+, withKeePassBrowserPasskeys ? true
 , withKeePassFDOSecrets ? true
 , withKeePassKeeShare ? true
 , withKeePassNetworking ? true
@ -70,6 +71,7 @@ stdenv.mkDerivation rec {
  ++ (lib.optional (withKeePassFDOSecrets && stdenv.isLinux) "-DWITH_XC_FDOSECRETS=ON")
  ++ (lib.optional (withKeePassYubiKey && stdenv.isLinux) "-DWITH_XC_YUBIKEY=ON")
  ++ (lib.optional withKeePassBrowser "-DWITH_XC_BROWSER=ON")
+  ++ (lib.optional withKeePassBrowserPasskeys "-DWITH_XC_BROWSER_PASSKEYS=ON")
  ++ (lib.optional withKeePassKeeShare "-DWITH_XC_KEESHARE=ON")
  ++ (lib.optional withKeePassNetworking "-DWITH_XC_NETWORKING=ON")
  ++ (lib.optional withKeePassSSHAgent "-DWITH_XC_SSHAGENT=ON");
--- a/pkgs/applications/misc/qlcplus/default.nix
+++ b/pkgs/applications/misc/qlcplus/default.nix
@ -1,30 +1,22 @@
 { lib, mkDerivation, fetchFromGitHub, fetchpatch, qmake, pkg-config, udev
-, qtmultimedia, qtscript, alsa-lib, ola, libftdi1, libusb-compat-0_1
+, qtmultimedia, qtscript, qtserialport, alsa-lib, ola, libftdi1, libusb-compat-0_1
 , libsndfile, libmad
 }:

 mkDerivation rec {
  pname = "qlcplus";
-  version = "4.12.3";
+  version = "4.13.0";

  src = fetchFromGitHub {
    owner = "mcallegari";
    repo = "qlcplus";
    rev = "QLC+_${version}";
-    sha256 = "PB1Y8N1TrJMcS7A2e1nKjsUlAxOYjdJqBhbyuDCAbGs=";
+    sha256 = "11av9hg6l0pb1lmlw35v1v2q9mmqz65yfaq01454y5qlmsbxpgkp";
  };

-  patches = [
-    (fetchpatch {
-      name = "qt5.15-deprecation-fixes.patch";
-      url = "https://github.com/mcallegari/qlcplus/commit/e4ce4b0226715876e8e9e3b23785d43689b2bb64.patch";
-      sha256 = "1zhrg6ava1nyc97xcx75r02zzkxmar0973w4jwkm5ch3iqa8bqnh";
-    })
-  ];
-
  nativeBuildInputs = [ qmake pkg-config ];
  buildInputs = [
-    udev qtmultimedia qtscript alsa-lib ola libftdi1 libusb-compat-0_1 libsndfile libmad
+    udev qtmultimedia qtscript qtserialport alsa-lib ola libftdi1 libusb-compat-0_1 libsndfile libmad
  ];

  qmakeFlags = [ "INSTALLROOT=$(out)" ];
--- a/pkgs/applications/networking/browsers/microsoft-edge/browser.nix
+++ b/pkgs/applications/networking/browsers/microsoft-edge/browser.nix
@ -33,6 +33,7 @@
 , libuuid
 , systemd
 , wayland
+, libGL

 # command line arguments which are always set e.g "--disable-gpu"
 , commandLineArgs ? ""
@ -93,7 +94,7 @@ stdenv.mkDerivation rec {
        glib nss nspr
      ];
      libGLESv2 = lib.makeLibraryPath [
-        xorg.libX11 xorg.libXext xorg.libxcb wayland
+        xorg.libX11 xorg.libXext xorg.libxcb wayland libGL
      ];
      liboneauth = lib.makeLibraryPath [
        libuuid xorg.libX11
--- a/pkgs/applications/networking/browsers/vivaldi/default.nix
+++ b/pkgs/applications/networking/browsers/vivaldi/default.nix
@ -24,7 +24,7 @@ let
  vivaldiName = if isSnapshot then "vivaldi-snapshot" else "vivaldi";
 in stdenv.mkDerivation rec {
  pname = "vivaldi";
-  version = "6.6.3271.53";
+  version = "6.6.3271.55";

  suffix = {
    aarch64-linux = "arm64";
@ -34,8 +34,8 @@ in stdenv.mkDerivation rec {
  src = fetchurl {
    url = "https://downloads.vivaldi.com/${branch}/vivaldi-${branch}_${version}-1_${suffix}.deb";
    hash = {
-      aarch64-linux = "sha256-iB8BPA7A2S9fsg5n6QDt6iKFnS1lQ6Xp2yO9VBGndq8=";
-      x86_64-linux = "sha256-2HS8SxaKu0NF++J8PhGJWEbA9FU1a+g/t9+HIKjvt58=";
+      aarch64-linux = "sha256-IqCmDqcZDLT1abx67gAsGHR8DVVIAGZ/sifZi8bxUNc=";
+      x86_64-linux = "sha256-n0CHm1Dtd2QhGNhI/9WzQ6CeCyMAHkBpOMC2w3ylk2g=";
    }.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
  };

--- a/pkgs/applications/networking/cluster/popeye/default.nix
+++ b/pkgs/applications/networking/cluster/popeye/default.nix
@ -2,13 +2,13 @@

 buildGoModule rec {
  pname = "popeye";
-  version = "0.21.2";
+  version = "0.21.3";

  src = fetchFromGitHub {
    rev = "v${version}";
    owner = "derailed";
    repo = "popeye";
-    sha256 = "sha256-NhQER6XeicpQY0rYisGvkUCHYsURJqt6xVKc9F0CmtE=";
+    sha256 = "sha256-2+AV2gt67zLa7bRIfsxQIeB82iJba8Y4P0fq9273r7Q=";
  };

  ldflags = [
--- a/pkgs/applications/office/gnucash/default.nix
+++ b/pkgs/applications/office/gnucash/default.nix
@ -28,12 +28,12 @@

 stdenv.mkDerivation rec {
  pname = "gnucash";
-  version = "5.5";
+  version = "5.6";

  # raw source code doesn't work out of box; fetchFromGitHub not usable
  src = fetchurl {
    url = "https://github.com/Gnucash/gnucash/releases/download/${version}/gnucash-${version}.tar.bz2";
-    hash = "sha256-tNr2e7iStwYyP2Lp+pckIDnX3QouHhB3HgwlgX3Q7Ts=";
+    hash = "sha256-tLQsYmNQ8+effKHyFzVFzGPd7hrd8kYLGh8iIhvyG9E=";
  };

  nativeBuildInputs = [
@ -99,7 +99,7 @@ stdenv.mkDerivation rec {
      owner = "Gnucash";
      repo = "gnucash-docs";
      rev = version;
-      hash = "sha256-ilDh4PH+tdrJReIpgvEd0Gvs8Xvt5Q43XM5r7Bn+5IM=";
+      hash = "sha256-rQZoau466Bi/YpPj1XpSsm67FgTYhiMfZfogTtn+m1k=";
    };

    nativeBuildInputs = [ cmake ];
--- a/pkgs/applications/science/electronics/kicad/base.nix
+++ b/pkgs/applications/science/electronics/kicad/base.nix
@ -204,7 +204,7 @@ stdenv.mkDerivation rec {
      Just the build products, the libraries are passed via an env var in the wrapper, default.nix
    '';
    homepage = "https://www.kicad.org/";
-    license = lib.licenses.agpl3Plus;
+    license = lib.licenses.gpl3Plus;
    platforms = lib.platforms.all;
  };
 }
--- a/pkgs/applications/version-management/ghq/default.nix
+++ b/pkgs/applications/version-management/ghq/default.nix
@ -2,16 +2,16 @@

 buildGoModule rec {
  pname = "ghq";
-  version = "1.5.0";
+  version = "1.6.0";

  src = fetchFromGitHub {
    owner = "x-motemen";
    repo = "ghq";
    rev = "v${version}";
-    sha256 = "sha256-l+Ycts7PSKR72GsHJ1zWqpyd0BMMib/GTUv+B0x6d8M=";
+    sha256 = "sha256-gSMSn7YuhV/m5po+nu9Z/bxSRKg7/fXbF1stm7JQqZI=";
  };

-  vendorHash = "sha256-6ZDvU3RQ/1M4DZMFOaQsEuodldB8k+2thXNhvZlVQEg=";
+  vendorHash = "sha256-M9B19rSEMnmT4wfOVnSAK06UPR/xrs0252lX3B9ebF8=";

  doCheck = false;

--- a/pkgs/applications/video/freetube/default.nix
+++ b/pkgs/applications/video/freetube/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  pname = "freetube";
-  version = "0.19.2";
+  version = "0.20.0";

  src = fetchurl {
    url = "https://github.com/FreeTubeApp/FreeTube/releases/download/v${version}-beta/freetube_${version}_amd64.AppImage";
-    sha256 = "sha256-GhlU02CmglHUzVTqoajXFS1E6WXxXjxRTdiDEDqsH8s=";
+    sha256 = "sha256-7k5hyiK3m+117AxmsoecGsgXSxs8xhyTf8+rl4oBbB8=";
  };

  passthru.tests = nixosTests.freetube;
--- a/pkgs/applications/video/kodi/addons/youtube/default.nix
+++ b/pkgs/applications/video/kodi/addons/youtube/default.nix
@ -3,13 +3,13 @@
 buildKodiAddon rec {
  pname = "youtube";
  namespace = "plugin.video.youtube";
-  version = "7.0.4";
+  version = "7.0.5";

  src = fetchFromGitHub {
    owner = "anxdpanic";
    repo = "plugin.video.youtube";
    rev = "v${version}";
-    hash = "sha256-vBDFxsbYemJKxWa7De++UB0E4t1Eo0PW6Glbw6+FK1w=";
+    hash = "sha256-oM1n0Rye2QagxXoAZ/6mXKeGqKjEdewgS79lhp+yCQI=";
  };

  propagatedBuildInputs = [
--- a/pkgs/build-support/dotnet/nuget-to-nix/nuget-to-nix.sh
+++ b/pkgs/build-support/dotnet/nuget-to-nix/nuget-to-nix.sh
@ -33,9 +33,13 @@ for index in "${sources[@]}"; do

    remote_sources+=($index)

-    base_addresses[$index]=$(
+    base_address=$(
    curl --compressed --netrc -fsL "$index" | \
      jq -r '.resources[] | select(."@type" == "PackageBaseAddress/3.0.0")."@id"')
+    if [[ ! "$base_address" == */ ]]; then
+      base_address="$base_address/"
+    fi
+    base_addresses[$index]="$base_address"
 done

 echo "{ fetchNuGet }: ["
--- a/pkgs/build-support/pkg-config-wrapper/default.nix
+++ b/pkgs/build-support/pkg-config-wrapper/default.nix
@ -34,6 +34,7 @@ let
  # See description in cc-wrapper.
  suffixSalt = replaceStrings ["-" "."] ["_" "_"] targetPlatform.config;

+  wrapperBinName = "${targetPrefix}${baseBinName}";
 in

 stdenv.mkDerivation {
@ -73,7 +74,7 @@ stdenv.mkDerivation {

      echo $pkg-config > $out/nix-support/orig-pkg-config

-      wrap ${targetPrefix}${baseBinName} ${./pkg-config-wrapper.sh} "${getBin pkg-config}/bin/${baseBinName}"
+      wrap ${wrapperBinName} ${./pkg-config-wrapper.sh} "${getBin pkg-config}/bin/${baseBinName}"
    ''
    # symlink in share for autoconf to find macros

@ -128,10 +129,11 @@ stdenv.mkDerivation {

  meta =
    let pkg-config_ = optionalAttrs (pkg-config != null) pkg-config; in
-    (optionalAttrs (pkg-config_ ? meta) (removeAttrs pkg-config.meta ["priority"])) //
+    (optionalAttrs (pkg-config_ ? meta) (removeAttrs pkg-config.meta ["priority" "mainProgram"])) //
    { description =
        attrByPath ["meta" "description"] "pkg-config" pkg-config_
        + " (wrapper script)";
      priority = 10;
+      mainProgram = wrapperBinName;
  };
 }
--- a/pkgs/by-name/bo/boxbuddy/package.nix
+++ b/pkgs/by-name/bo/boxbuddy/package.nix
@ -9,16 +9,16 @@

 rustPlatform.buildRustPackage rec {
  pname = "boxbuddy";
-  version = "2.2.0";
+  version = "2.2.2";

  src = fetchFromGitHub {
    owner = "Dvlv";
    repo = "BoxBuddyRS";
    rev = version;
-    hash = "sha256-Fb3Df+P2ovSVQhtDxhed/hH06UKnJY/iugt3Pi9/Jp0=";
+    hash = "sha256-y3QfNOaeeZ4Vvby4SkyVgTCL8qIYvXpcK1c8ofzjrj0=";
  };

-  cargoHash = "sha256-dmBQdE4rsL8ygXOGupjtZrWuXjVAy5m1p/xJlUdUwkY=";
+  cargoHash = "sha256-53hndNIcGtU8Uxnyh8y5v+0wURflNzlzwuyoh+HUXD4=";

  # The software assumes it is installed either in flatpak or in the home directory
  # so the xdg data path needs to be patched here
--- a/pkgs/by-name/c2/c2fmzq/package.nix
+++ b/pkgs/by-name/c2/c2fmzq/package.nix
@ -6,20 +6,20 @@

 buildGoModule rec {
  pname = "c2FmZQ";
-  version = "0.4.18";
+  version = "0.4.19";

  src = fetchFromGitHub {
    owner = "c2FmZQ";
    repo = "c2FmZQ";
    rev = "v${version}";
-    hash = "sha256-CWtQMXICCyuXbknR1Z2sLe7GyqN0F2sQGtiTnqppnVA=";
+    hash = "sha256-9kCiV+v7RNFDrAbWRujTW9b9sbYX9fGEE37S9uDp0nY=";
  };

  ldflags = [ "-s" "-w" ];

  sourceRoot = "${src.name}/c2FmZQ";

-  vendorHash = "sha256-cTXSFwWGHV2QJM4mX/Z+ZxCXKwr+59lEPvJa/PTA1wU=";
+  vendorHash = "sha256-plORJl7KNsBP3tQSYX8829+sb8l0sO/TS8Bt25JXNgY=";

  subPackages = [ "c2FmZQ-client" "c2FmZQ-server" ];

--- a/pkgs/by-name/ce/centerpiece/package.nix
+++ b/pkgs/by-name/ce/centerpiece/package.nix
@ -0,0 +1,55 @@
+{ lib
+, stdenv
+, pkg-config
+, dbus
+, vulkan-loader
+, libGL
+, fetchFromGitHub
+, rustPlatform
+, libxkbcommon
+, wayland
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "centerpiece";
+  version = "1.0.0";
+
+  src = fetchFromGitHub {
+    owner = "friedow";
+    repo = "centerpiece";
+    rev = "v${version}";
+    hash = "sha256-I630XrmyRAjVxFvISo2eIUP3YmivZovnV89Xsx5OduY=";
+  };
+
+  cargoHash = "sha256-yvvMe1zBUREqRzp/0zYsu7AoXS9Jqq67DY5uMParhEs=";
+
+  nativeBuildInputs = [ pkg-config ];
+  buildInputs = [
+    dbus
+    libGL
+    libxkbcommon
+    vulkan-loader
+    wayland
+  ];
+
+  postFixup = lib.optional stdenv.isLinux ''
+    rpath=$(patchelf --print-rpath $out/bin/centerpiece)
+    patchelf --set-rpath "$rpath:${
+      lib.makeLibraryPath [
+        libGL
+        libxkbcommon
+        vulkan-loader
+        wayland
+      ]
+    }" $out/bin/centerpiece
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/friedow/centerpiece";
+    description = "Your trusty omnibox search";
+    license = licenses.mit;
+    maintainers = with maintainers; [ a-kenji ];
+    platforms = platforms.linux;
+    mainProgram = "centerpiece";
+  };
+}
--- a/pkgs/by-name/da/daytona-bin/package.nix
+++ b/pkgs/by-name/da/daytona-bin/package.nix
@ -50,6 +50,7 @@ stdenvNoCC.mkDerivation (finalAttrs: {
    license = lib.licenses.asl20;
    mainProgram = "daytona";
    maintainers = with lib.maintainers; [ ];
+    platforms = lib.platforms.linux ++ lib.platforms.darwin;
    sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ];
  };
 })
--- a/pkgs/by-name/di/dissent/package.nix
+++ b/pkgs/by-name/di/dissent/package.nix
@ -18,13 +18,13 @@

 buildGoModule rec {
  pname = "dissent";
-  version = "0.0.22";
+  version = "0.0.23";

  src = fetchFromGitHub {
    owner = "diamondburned";
    repo = "dissent";
    rev = "v${version}";
-    hash = "sha256-HNNTF/a+sLFp+HCxltYRuDssoLnIhzEXuDLKTPxWzeM=";
+    hash = "sha256-aHY2XmrJv2SSoXIKj63xu6t+Yzaur/6OJUFKga7DWDg=";
  };

  nativeBuildInputs = [
--- a/pkgs/by-name/fo/folio/package.nix
+++ b/pkgs/by-name/fo/folio/package.nix
@ -15,13 +15,13 @@

 stdenv.mkDerivation rec {
  pname = "folio";
-  version = "24.09";
+  version = "24.10";

  src = fetchFromGitHub {
    owner = "toolstack";
    repo = "Folio";
    rev = version;
-    hash = "sha256-D9jjoOVDJa90tpb8AW93xLyXW/meyMp1pCYK52DsJN0=";
+    hash = "sha256-v9YtMFVjRtsf+dijAM5mULx15sOn0u3b/fmRiOAtawc=";
  };

  nativeBuildInputs = [
--- a/pkgs/by-name/gf/gfal2-util/package.nix
+++ b/pkgs/by-name/gf/gfal2-util/package.nix
@ -0,0 +1,2 @@
+{ python3Packages }:
+with python3Packages; toPythonApplication gfal2-util
--- a/pkgs/by-name/gf/gfal2/package.nix
+++ b/pkgs/by-name/gf/gfal2/package.nix
@ -0,0 +1,129 @@
+{ lib
+, stdenv
+, callPackage
+, fetchFromGitHub
+  # Native build inputs
+, cmake
+, pkg-config
+  # General build inputs
+, glib
+, gtest
+, json_c
+, openldap
+  # Plugin build inputs
+, cryptopp
+, davix-copy
+, dcap
+, libssh2
+, libuuid
+, pugixml
+, xrootd
+  # For enablePluginStatus.https only
+, gsoap
+}:
+stdenv.mkDerivation (finalAttrs: {
+  pname = "gfal2";
+  version = "2.22.2";
+
+  src = fetchFromGitHub {
+    owner = "cern-fts";
+    repo = "gfal2";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-xcM29mZRUrnSE0//rHMaJFgPBeT6E4WdB9tCFa/y5+g=";
+  };
+
+  passthru.enablePluginStatus = {
+    # TODO: Change back to `true` once dcap is fixed on Darwin.
+    dcap = !dcap.meta.broken;
+    file = true;
+    gridftp = false;
+    # davix-copy's dependency gsoap is currently only available on Linux.
+    # TODO: Change back to `true` once gsoap is fixed on Darwin.
+    http = lib.meta.availableOn stdenv.hostPlatform gsoap;
+    lfc = false;
+    # Break because of redundant `-luuid`. This needs to be fixed from the gfal2 upstream.
+    # TODO: Change back to `true` once fixed.
+    mock = !stdenv.isDarwin;
+    rfio = false;
+    sftp = true;
+    srm = false;
+    xrootd = true;
+  };
+
+  passthru.tests = (
+    # Enable only one plugin in each test case,
+    # to ensure that they gets their dependency when invoked separately.
+    lib.listToAttrs
+      (map
+        (pluginName: lib.nameValuePair
+          "gfal2-${pluginName}"
+          (finalAttrs.finalPackage.overrideAttrs (previousAttrs: {
+            passthru = previousAttrs.passthru // {
+              enablePluginStatus = lib.mapAttrs (n: v: n == pluginName) previousAttrs.passthru.enablePluginStatus;
+            };
+          })))
+        (lib.filter (lib.flip lib.getAttr finalAttrs.passthru.enablePluginStatus) (lib.attrNames finalAttrs.passthru.enablePluginStatus))
+      )
+  ) // {
+    # Disable all plugins in this test case.
+    gfal2-minimal = finalAttrs.finalPackage.overrideAttrs (previousAttrs: {
+      passthru.enablePluginStatus = lib.mapAttrs (n: v: false) previousAttrs.passthru.enablePluginStatus;
+    });
+  };
+
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+  ];
+
+  buildInputs = lib.unique (
+    [
+      glib
+      json_c
+      # gfal2 version older than 2.21.1 fails to see openldap 2.5+
+      # and will complain
+      # bin/ld: cannot find -lldap_r: No such file or directory
+      # See https://github.com/cern-fts/gfal2/blob/aa24462bb67e259e525f26fb5feb97050a8c5c61/RELEASE-NOTES
+      openldap
+      pugixml # Optional, for MDS Cache.
+    ]
+    ++ lib.optionals finalAttrs.passthru.enablePluginStatus.dcap [ dcap ]
+    ++ lib.optionals finalAttrs.passthru.enablePluginStatus.http [ cryptopp davix-copy ]
+    ++ lib.optionals finalAttrs.passthru.enablePluginStatus.mock [ libuuid ]
+    ++ lib.optionals finalAttrs.passthru.enablePluginStatus.sftp [ libssh2 ]
+    ++ lib.optionals finalAttrs.passthru.enablePluginStatus.xrootd [ xrootd libuuid ]
+  );
+
+  cmakeFlags = (
+    map
+      (pluginName: "-DPLUGIN_${lib.toUpper pluginName}=${lib.toUpper (lib.boolToString finalAttrs.passthru.enablePluginStatus.${pluginName})}")
+      (lib.attrNames finalAttrs.passthru.enablePluginStatus)
+  )
+  ++ [ "-DSKIP_TESTS=${lib.toUpper (lib.boolToString (!finalAttrs.doCheck))}" ]
+  ++ lib.optionals finalAttrs.doCheck [ "-DGTEST_INCLUDE_DIR=${gtest.dev}/include" ]
+  ++ lib.optionals finalAttrs.passthru.enablePluginStatus.http [ "-DCRYPTOPP_INCLUDE_DIRS=${cryptopp.dev}/include/cryptopp" ]
+  ++ lib.optionals finalAttrs.passthru.enablePluginStatus.xrootd [ "-DXROOTD_INCLUDE_DIR=${xrootd.dev}/include/xrootd" ]
+  ;
+
+  doCheck = stdenv.hostPlatform.isLinux;
+
+  checkInputs = [
+    gtest
+  ];
+
+  meta = with lib; {
+    description = "Multi-protocol data management library by CERN";
+    longDescription = ''
+      GFAL (Grid File Access Library )
+      is a C library providing an abstraction layer of
+      the grid storage system complexity.
+      The complexity of the grid is hidden from the client side
+      behind a simple common POSIX API.
+    '';
+    homepage = "https://github.com/cern-fts/gfal2";
+    license = licenses.asl20;
+    platforms = platforms.all;
+    maintainers = with maintainers; [ ShamrockLee ];
+    mainProgram = "gfal2";
+  };
+})
--- a/pkgs/by-name/gi/git-gr/package.nix
+++ b/pkgs/by-name/gi/git-gr/package.nix
@ -8,12 +8,14 @@
  libiconv,
  darwin,
  nix-update-script,
+  pkg-config,
+  openssl,
 }:
 let
  canRunGitGr = stdenv.hostPlatform.emulatorAvailable buildPackages;
  gitGr = "${stdenv.hostPlatform.emulator buildPackages} $out/bin/git-gr";
  pname = "git-gr";
-  version = "1.0.3";
+  version = "1.2.1";
 in
 rustPlatform.buildRustPackage {
  inherit pname version;
@ -22,18 +24,25 @@ rustPlatform.buildRustPackage {
    owner = "9999years";
    repo = pname;
    rev = "refs/tags/v${version}";
-    hash = "sha256-hvK4reFR60q9mw3EdNLav9VMr4H6Zabv1N1D/5AAKuQ=";
+    hash = "sha256-5Pr1z+RmY92cfT7KtFnUKpzhniUN6RjDKBekWiYCCuU=";
  };

  buildFeatures = [ "clap_mangen" ];

-  cargoHash = "sha256-efoRiPWugz955MflIS81Nie7Oq5Y4u5CI+/el8fJVl0=";
+  cargoHash = "sha256-5JLTSBBTPGUbuqUql/cMJKBLlO2uzuU1EDhfScaeCUg=";
+
+  OPENSSL_NO_VENDOR = true;

  nativeBuildInputs =
-    [ installShellFiles ]
+    [installShellFiles]
+    ++ lib.optional stdenv.isLinux pkg-config;
+
+  buildInputs =
+    lib.optional stdenv.isLinux openssl
    ++ lib.optionals stdenv.isDarwin [
      libiconv
      darwin.apple_sdk.frameworks.CoreServices
+      darwin.apple_sdk.frameworks.SystemConfiguration
    ];

  postInstall = lib.optionalString canRunGitGr ''
--- a/pkgs/applications/misc/gpscorrelate/default.nix
+++ b/pkgs/applications/misc/gpscorrelate/default.nix
@ -1,25 +1,29 @@
-{ lib, stdenv, fetchFromGitHub, fetchpatch, pkg-config, exiv2, libxml2, gtk3
-, libxslt, docbook_xsl, docbook_xml_dtd_42, desktop-file-utils, wrapGAppsHook }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, pkg-config
+, exiv2
+, libxml2
+, gtk3
+, libxslt
+, docbook_xsl
+, docbook_xml_dtd_42
+, desktop-file-utils
+, wrapGAppsHook
+, desktopToDarwinBundle
+}:

 stdenv.mkDerivation rec {
  pname = "gpscorrelate";
-  version = "2.0";
+  version = "2.1";

  src = fetchFromGitHub {
    owner = "dfandrich";
-    repo = pname;
+    repo = "gpscorrelate";
    rev = version;
-    sha256 = "1wkpb0nqnm0ik46hp2sibf96h2gxi6n951zm8c72scgmh4ciq4fl";
+    sha256 = "sha256-1t9XUY12hVaUNOg785dMJCiaMMCI2XCcif1DkKYXOoo=";
  };

-  patches = [
-    (fetchpatch {
-      name = "gpscorrelate-2.0-exiv2-0.28.patch";
-      url = "https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-geosciences/gpscorrelate/files/gpscorrelate-2.0-exiv2-0.28.patch?id=002882203ad6a2b08ce035a18b95844a9f4b85d0";
-      hash = "sha256-/5czvSh2siPmohXWHQEg6VWCUQnZxEm2livLsEOAa6c=";
-    })
-  ];
-
  nativeBuildInputs = [
    desktop-file-utils
    docbook_xml_dtd_42
@ -27,7 +31,7 @@ stdenv.mkDerivation rec {
    libxslt
    pkg-config
    wrapGAppsHook
-  ];
+  ] ++ lib.optional stdenv.isDarwin desktopToDarwinBundle;

  buildInputs = [
    exiv2
--- a/pkgs/by-name/kn/knossosnet/package.nix
+++ b/pkgs/by-name/kn/knossosnet/package.nix
@ -10,13 +10,13 @@

 buildDotnetModule rec {
  pname = "knossosnet";
-  version = "1.0.0";
+  version = "1.1.0";

  src = fetchFromGitHub {
    owner = "KnossosNET";
    repo = "Knossos.NET";
    rev = "v${version}";
-    hash = "sha256-Wq4WeRf+ELTxZhQyQf6XAOPmbJwX06qQ5GxRnnK3lyI=";
+    hash = "sha256-5pHBCqAEuZDt5lIkLlFN2zKRZkRybc3mUMqsTN44EwU=";
  };

  patches = [ ./targetframework.patch ];
--- a/pkgs/by-name/ko/komac/package.nix
+++ b/pkgs/by-name/ko/komac/package.nix
@ -0,0 +1,45 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, rustPlatform
+, darwin
+, testers
+, komac
+}:
+
+let
+  version = "2.1.0";
+  src = fetchFromGitHub {
+    owner = "russellbanks";
+    repo = "Komac";
+    rev = "v${version}";
+    hash = "sha256-L8UYpNqjRyqf4hPQwD9LaXWu6jYaP34yTwTxcqg+e2U=";
+  };
+in
+rustPlatform.buildRustPackage {
+  inherit version src;
+
+  pname = "komac";
+
+  cargoHash = "sha256-J4QZzbyDr4SDt6LlAy9ZdpqgIufZCZHmOC9eu70wMsM=";
+
+  buildInputs = lib.optionals stdenv.isDarwin [
+    darwin.apple_sdk.frameworks.SystemConfiguration
+  ];
+
+  passthru.tests.version = testers.testVersion {
+    inherit version;
+
+    package = komac;
+    command = "komac --version";
+  };
+
+  meta = with lib; {
+    description = "The Community Manifest Creator for WinGet";
+    homepage = "https://github.com/russellbanks/Komac";
+    changelog = "https://github.com/russellbanks/Komac/releases/tag/${src.rev}";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ kachick ];
+    mainProgram = "komac";
+  };
+}
--- a/pkgs/by-name/or/orchard/package.nix
+++ b/pkgs/by-name/or/orchard/package.nix
@ -2,13 +2,13 @@

 buildGoModule rec {
  pname = "orchard";
-  version = "0.15.2";
+  version = "0.16.0";

  src = fetchFromGitHub {
    owner = "cirruslabs";
    repo = pname;
    rev = version;
-    hash = "sha256-ccmG94OrsfQDmyBKJiPPI97uMFlnL26epsVMdAqO/1o=";
+    hash = "sha256-XLml3/PoDS4BN+iApoEsjt1VPjsPEKTGTZcM7V5ZQaY=";
    # populate values that require us to use git. By doing this in postFetch we
    # can delete .git afterwards and maintain better reproducibility of the src.
    leaveDotGit = true;
--- a/pkgs/by-name/pd/pdk/Gemfile.lock
+++ b/pkgs/by-name/pd/pdk/Gemfile.lock
@ -58,7 +58,7 @@ GEM
    wisper (2.0.1)

 PLATFORMS
-  x86_64-linux
+  ruby

 DEPENDENCIES
  pdk (= 3.0.1)
--- a/pkgs/by-name/re/renode-unstable/package.nix
+++ b/pkgs/by-name/re/renode-unstable/package.nix
@ -5,11 +5,11 @@

 renode.overrideAttrs (finalAttrs: _: {
  pname = "renode-unstable";
-  version = "1.15.0+20240323git3bd8e280d";
+  version = "1.15.0+20240404gitbfa16ba07";

  src = fetchurl {
    url = "https://builds.renode.io/renode-${finalAttrs.version}.linux-portable.tar.gz";
-    hash = "sha256-hIPBM9PE6vtqo8XJvOWS3mIa9Vr7v9bcMdXmeQzBYsk=";
+    hash = "sha256-pXA6sGYBlLU2EnhFvUwRWkYirMi5BTgzyUbQ33sIMrg=";
  };

  passthru.updateScript =
--- a/pkgs/by-name/re/restinio/package.nix
+++ b/pkgs/by-name/re/restinio/package.nix
@ -2,7 +2,6 @@
  lib,
  stdenv,
  fetchFromGitHub,
-  fetchpatch,
  cmake,
  asio,
  boost,
@ -22,39 +21,15 @@ assert !with_boost_asio -> asio != null;

 stdenv.mkDerivation (finalAttrs: {
  pname = "restinio";
-  version = "0.7.1";
+  version = "0.7.2";

  src = fetchFromGitHub {
    owner = "Stiffstream";
    repo = "restinio";
    rev = "v.${finalAttrs.version}";
-    hash = "sha256-XodG+dVW4iBgFx0Aq0+/pZyCLyqTBtW7e9r69y176Ro=";
+    hash = "sha256-Nv/VVdHciCv+DsVu3MqfXeAa8Ef+qi6c1OaTAVrYUg0=";
  };

-  patches = let
-    useCommit = {id, name, hash}:
-    fetchpatch {
-      inherit name hash;
-      url = "https://github.com/Stiffstream/restinio/commit/${id}.patch";
-    };
-  in [
-    (useCommit {
-      id = "57e6ae3f73a03a5120feb80a7bb5dca27179fa38";
-      name = "restinio-unvendor-catch2_part1.patch";
-      hash = "sha256-2Htt9WTP6nrh+1y7y2xleFj568IpnSEn9Qhb1ObLam8=";
-    })
-    (useCommit {
-      id = "0060e493b99f03c38dda519763f6d6701bc18112";
-      name = "restinio-unvendor-catch2_part2.patch";
-      hash = "sha256-Eg/VNxPwNtEYmalP5myn+QvqwU6wln9v0vxbRelRHA8=";
-    })
-    (useCommit {
-      id = "05bea25f82917602a49b72b8ea10eeb43984762f";
-      name = "restinio-unvendor-catch2_part3.patch";
-      hash = "sha256-fA+U/Y7FyrxDRiWSVXCy9dMF4gmfDLag7gBWoY74In0=";
-    })
-  ];
-
  strictDeps = true;

  nativeBuildInputs = [ cmake ];
--- a/pkgs/by-name/rn/rnd-name/package.nix
+++ b/pkgs/by-name/rn/rnd-name/package.nix
@ -0,0 +1,33 @@
+{ lib
+, buildGoModule
+, fetchFromGitHub
+, nix-update-script
+}:
+let
+  version = "1.0.0";
+in
+buildGoModule {
+  inherit version;
+  pname = "rnd-name";
+
+  src = fetchFromGitHub {
+    owner = "mrhenry";
+    repo = "rnd-name";
+    rev = "v${version}";
+    hash = "sha256-o3A7VDH6rpJmCBu8ZPfPllMm1rAN1tNrz2eUyd2Tjjs=";
+  };
+
+  vendorHash = null;
+
+  passthru.updateScript = nix-update-script { };
+
+  meta = {
+    platforms = lib.platforms.all;
+    mainProgram = "rnd-name";
+    description = "Random strings that are easy to recognize";
+    homepage = "https://github.com/mrhenry/rnd-name";
+    changelog = "https://github.com/mrhenry/rnd-name/releases/tag/v${version}";
+    license = lib.licenses.mit0;
+    maintainers = with lib.maintainers; [ fd ];
+  };
+}
--- a/pkgs/by-name/sa/satty/package.nix
+++ b/pkgs/by-name/sa/satty/package.nix
@ -16,16 +16,16 @@
 rustPlatform.buildRustPackage rec {

  pname = "satty";
-  version = "0.11.3";
+  version = "0.12.0";

  src = fetchFromGitHub {
    owner = "gabm";
    repo = "Satty";
    rev = "v${version}";
-    hash = "sha256-TKpotVVjXWm2uue4a4QEqVH/qHKSsegL2MNcsnk0CHw=";
+    hash = "sha256-yidnpgUwfbaKmWznjN+TkF6ww/gVLDXFjQ0cIAQ4qFM=";
  };

-  cargoHash = "sha256-0AyzjKkTNZwGCT73Xo5AY7rPJwQ9GgAxtMf6lJnrTSA=";
+  cargoHash = "sha256-GP7Bu11xim9lAfdhgm+MAxBghd5taA+Q0cWCbI8OxEM=";

  nativeBuildInputs = [
    copyDesktopItems
--- a/pkgs/by-name/si/silverbullet/package.nix
+++ b/pkgs/by-name/si/silverbullet/package.nix
@ -0,0 +1,39 @@
+{ lib
+, stdenv
+, fetchurl
+, deno
+, makeWrapper
+}:
+stdenv.mkDerivation (finalAttrs: {
+  pname = "silverbullet";
+  version = "0.7.6";
+
+  src = fetchurl {
+    url = "https://github.com/silverbulletmd/silverbullet/releases/download/${finalAttrs.version}/silverbullet.js";
+    hash = "sha256-bnD9iZVRIg6otgDi4yNWySqmJsJJIVnjFGsTrGCMw/o=";
+  };
+
+  dontUnpack = true;
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out/{bin,lib}
+    cp $src $out/lib/silverbullet.js
+    makeWrapper ${lib.getExe deno} $out/bin/silverbullet \
+        --set DENO_NO_UPDATE_CHECK "1" \
+        --add-flags "run -A --unstable-kv --unstable-worker-options ${placeholder "out"}/lib/silverbullet.js"
+    runHook postInstall
+  '';
+
+  meta = {
+    changelog = "https://github.com/silverbulletmd/silverbullet/blob/${finalAttrs.version}/website/CHANGELOG.md";
+    description = "An open-source, self-hosted, offline-capable Personal Knowledge Management (PKM) web application";
+    homepage = "https://silverbullet.md";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ aorith ];
+    mainProgram = "silverbullet";
+    inherit (deno.meta) platforms;
+  };
+})
--- a/pkgs/by-name/sp/spicetify-cli/package.nix
+++ b/pkgs/by-name/sp/spicetify-cli/package.nix
@ -2,13 +2,13 @@

 buildGoModule rec {
  pname = "spicetify-cli";
-  version = "2.36.0";
+  version = "2.36.2";

  src = fetchFromGitHub {
    owner = "spicetify";
    repo = "spicetify-cli";
    rev = "v${version}";
-    hash = "sha256-Eth/ihsn/+XVi3YtOdnyzbvMkpR1RBX9Tz7RFQr8MzU=";
+    hash = "sha256-M+jx7FGq73eTFdBuCC/HxZq03bRIwlx1Nuz9fYQ0xfI=";
  };

  vendorHash = "sha256-axE1SY+UW5oddyhOiktq+vNfhw2/SFX4ut4Hivg6TYQ=";
--- a/pkgs/by-name/st/stirling-pdf/package.nix
+++ b/pkgs/by-name/st/stirling-pdf/package.nix
@ -11,13 +11,13 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "stirling-pdf";
-  version = "0.22.3";
+  version = "0.22.7";

  src = fetchFromGitHub {
    owner = "Stirling-Tools";
    repo = "Stirling-PDF";
    rev = "v${finalAttrs.version}";
-    hash = "sha256-8zXTapFAXw4+KLLirxBeEBmqNw6ILFHtbsaBSP3Ehyg=";
+    hash = "sha256-BB9O5nf47IrBbrnjU1sWw6xKT4XR1c+fWrno4liH5Xs=";
  };

  patches = [
@ -75,7 +75,7 @@ stdenv.mkDerivation (finalAttrs: {

    outputHashAlgo = "sha256";
    outputHashMode = "recursive";
-    outputHash = "sha256-zUzKSa7zuIoXE77Hk/Xr5iMF4CEumV9horW2BTFRdtE=";
+    outputHash = "sha256-8suWAX1+GGMvMUaymZnze7cBL701P/381dGqnyfha7s=";
  };

  nativeBuildInputs = [
--- a/pkgs/applications/file-managers/tuifimanager/default.nix
+++ b/pkgs/applications/file-managers/tuifimanager/default.nix
@ -4,7 +4,7 @@
 }:

 python3.pkgs.buildPythonApplication rec {
-  pname = "tuifi-manager";
+  pname = "tuifimanager";
  version = "3.3.5";
  format = "pyproject";

@ -41,7 +41,7 @@ python3.pkgs.buildPythonApplication rec {
    homepage = "https://github.com/GiorgosXou/TUIFIManager";
    changelog = "https://github.com/GiorgosXou/TUIFIManager/blob/${src.rev}/CHANGELOG.md";
    license = licenses.gpl3Only;
-    maintainers = with maintainers; [ michaelBelsanti ];
+    maintainers = with maintainers; [ michaelBelsanti sigmanificient ];
    mainProgram = "tuifi";
  };
 }
--- a/pkgs/by-name/wi/wit-bindgen/package.nix
+++ b/pkgs/by-name/wi/wit-bindgen/package.nix
@ -5,16 +5,16 @@

 rustPlatform.buildRustPackage rec {
  pname = "wit-bindgen";
-  version = "0.23.0";
+  version = "0.24.0";

  src = fetchFromGitHub {
    owner = "bytecodealliance";
    repo = "wit-bindgen";
    rev = "v${version}";
-    hash = "sha256-xzLUBAtfCwBMpIqlUf8oSh3VqUy/SRgdEWsAw6CIbos=";
+    hash = "sha256-lH5ejZEEtGJbqBTAm0VO2ww+fh+fAtuRlTLfc58WFxc=";
  };

-  cargoHash = "sha256-gM32fmhMYaNu6rvvSTYTguDmLuY6oDUdVKclZlKttsQ=";
+  cargoHash = "sha256-bBA2AE8tN2J6SryZSBpDhFUxnMhWQmaqmU71QaTAYzY=";

  # Some tests fail because they need network access to install the `wasm32-unknown-unknown` target.
  # However, GitHub Actions ensures a proper build.
--- a/pkgs/data/themes/where-is-my-sddm-theme/default.nix
+++ b/pkgs/data/themes/where-is-my-sddm-theme/default.nix
@ -23,13 +23,13 @@ in

 stdenvNoCC.mkDerivation rec {
  pname = "where-is-my-sddm-theme";
-  version = "1.7.0";
+  version = "1.8.0";

  src = fetchFromGitHub {
    owner = "stepanzubkov";
    repo = pname;
    rev = "v${version}";
-    hash = "sha256-yj056ys+bDJ6snDW/clNyEQlkUPHE4A1pdwT76fItDI=";
+    hash = "sha256-/D3i4QcE5+GbiAw32bFYJ7UxW/5NAl9FqQfiQc4akzI=";
  };

  propagatedUserEnvPkgs = [ qtgraphicaleffects ];
--- a/pkgs/development/cuda-modules/setup-hooks/auto-add-driver-runpath-hook.sh
+++ b/pkgs/development/cuda-modules/setup-hooks/auto-add-driver-runpath-hook.sh
@ -1,8 +0,0 @@
-# shellcheck shell=bash
-# Run addDriverRunpath on all dynamically linked ELF files
-echo "Sourcing auto-add-driver-runpath-hook"
-
-if [ -z "${dontUseAutoAddDriverRunpath-}" ]; then
-  echo "Using autoAddDriverRunpath"
-  postFixupHooks+=("autoFixElfFiles addDriverRunpath")
-fi
--- a/pkgs/development/cuda-modules/setup-hooks/auto-fix-elf-files.sh
+++ b/pkgs/development/cuda-modules/setup-hooks/auto-fix-elf-files.sh
@ -1,64 +0,0 @@
-# shellcheck shell=bash
-# List all dynamically linked ELF files in the outputs and apply a generic fix
-# action provided as a parameter (currently used to add the CUDA or the
-# cuda_compat driver to the runpath of binaries)
-echo "Sourcing cuda/fix-elf-files.sh"
-
-# Returns the exit code of patchelf --print-rpath.
-# A return code of 0 (success) means the ELF file has a dynamic section, while
-# a non-zero return code means the ELF file is statically linked (or is not an
-# ELF file).
-elfHasDynamicSection() {
-  local libPath
-
-  if [[ $# -eq 0 ]]; then
-    echo "elfHasDynamicSection: no library path provided" >&2
-    exit 1
-  elif [[ $# -gt 1 ]]; then
-    echo "elfHasDynamicSection: too many arguments" >&2
-    exit 1
-  elif [[ "$1" == "" ]]; then
-    echo "elfHasDynamicSection: empty library path" >&2
-    exit 1
-  else
-    libPath="$1"
-    shift 1
-  fi
-
-  patchelf --print-rpath "$libPath" >& /dev/null
-  return $?
-}
-
-# Run a fix action on all dynamically linked ELF files in the outputs.
-autoFixElfFiles() {
-  local fixAction
-  local outputPaths
-
-  if [[ $# -eq 0 ]]; then
-    echo "autoFixElfFiles: no fix action provided" >&2
-    exit 1
-  elif [[ $# -gt 1 ]]; then
-    echo "autoFixElfFiles: too many arguments" >&2
-    exit 1
-  elif [[ "$1" == "" ]]; then
-    echo "autoFixElfFiles: empty fix action" >&2
-    exit 1
-  else
-    fixAction="$1"
-  fi
-
-  mapfile -t outputPaths < <(for o in $(getAllOutputNames); do echo "${!o}"; done)
-
-  find "${outputPaths[@]}" -type f -print0  | while IFS= read -rd "" f; do
-    if ! isELF "$f"; then
-      continue
-    elif elfHasDynamicSection "$f"; then
-      # patchelf returns an error on statically linked ELF files, and in
-      # practice fixing actions all involve patchelf
-      echo "autoFixElfFiles: using $fixAction to fix $f" >&2
-      $fixAction "$f"
-    elif (( "${NIX_DEBUG:-0}" >= 1 )); then
-      echo "autoFixElfFiles: skipping a statically-linked ELF file $f"
-    fi
-  done
-}
--- a/pkgs/development/cuda-modules/setup-hooks/extension.nix
+++ b/pkgs/development/cuda-modules/setup-hooks/extension.nix
@ -1,10 +1,10 @@
 final: _: {
-  # Helper hook used in both autoAddCudaCompatRunpath and
-  # autoAddDriverRunpath that applies a generic patching action to all elf
-  # files with a dynamic linking section.
-  autoFixElfFiles = final.callPackage (
-    { makeSetupHook }: makeSetupHook { name = "auto-fix-elf-files"; } ./auto-fix-elf-files.sh
-  ) { };
+  # TODO:
+  # - Move to cuda-modules/aliases.nix once
+  #   https://github.com/NixOS/nixpkgs/issues/141803 is ready.
+  # - Consider removing after 24.11.
+  inherit (final.pkgs) autoAddDriverRunpath autoFixElfFiles;
+  autoAddOpenGLRunpathHook = final.autoAddDriverRunpath;

  # Internal hook, used by cudatoolkit and cuda redist packages
  # to accommodate automatic CUDAToolkit_ROOT construction
@ -32,24 +32,6 @@ final: _: {
    ) { }
  );

-  autoAddDriverRunpath = final.callPackage (
-    {
-      addDriverRunpath,
-      autoFixElfFiles,
-      makeSetupHook,
-    }:
-    makeSetupHook {
-      name = "auto-add-opengl-runpath-hook";
-      propagatedBuildInputs = [
-        addDriverRunpath
-        autoFixElfFiles
-      ];
-    } ./auto-add-driver-runpath-hook.sh
-  ) { };
-
-  # Deprecated: an alias kept for compatibility. Consider removing after 24.11
-  autoAddOpenGLRunpathHook = final.autoAddDriverRunpath;
-
  # autoAddCudaCompatRunpath hook must be added AFTER `setupCudaHook`. Both
  # hooks prepend a path with `libcuda.so` to the `DT_RUNPATH` section of
  # patched elf files, but `cuda_compat` path must take precedence (otherwise,
--- a/pkgs/development/libraries/armadillo/default.nix
+++ b/pkgs/development/libraries/armadillo/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  pname = "armadillo";
-  version = "12.8.1";
+  version = "12.8.2";

  src = fetchurl {
    url = "mirror://sourceforge/arma/armadillo-${version}.tar.xz";
-    hash = "sha256-J4HdOmzF+aSckaRRnd4rHCQzWlv+DMHJiBtjYxQkUrQ=";
+    hash = "sha256-A7YvjAnk9ddGQ7R4UgdBuOJ7VefkUll4/K4vXXkaw78=";
  };

  nativeBuildInputs = [ cmake ];
--- a/pkgs/development/libraries/hunspell/dictionaries-chromium.nix
+++ b/pkgs/development/libraries/hunspell/dictionaries-chromium.nix
@ -67,4 +67,13 @@ rec {
    dictFileName = "de-DE-3-0.bdic";
    shortDescription = "German (Germany)";
  };
+
+  /* FRENCH */
+
+  fr_FR = fr-fr;
+  fr-fr = mkDictFromChromium {
+    shortName = "fr-fr";
+    dictFileName = "fr-FR-3-0.bdic";
+    shortDescription = "French (France)";
+  };
 }
--- a/pkgs/development/libraries/ldb/default.nix
+++ b/pkgs/development/libraries/ldb/default.nix
@ -17,11 +17,11 @@

 stdenv.mkDerivation rec {
  pname = "ldb";
-  version = "2.8.0";
+  version = "2.9.0";

  src = fetchurl {
    url = "mirror://samba/ldb/${pname}-${version}.tar.gz";
-    hash = "sha256-NY3KEPzScgeshXoNf0NaRtvGzR98ENu4QMGTG/GWXwg=";
+    hash = "sha256-EFqv9xrYgaf661gv1BauKCIbb94zj/+CgoBlBiwlB6U=";
  };

  outputs = [ "out" "dev" ];
--- a/pkgs/development/libraries/oneDNN/default.nix
+++ b/pkgs/development/libraries/oneDNN/default.nix
@ -9,13 +9,13 @@
 # https://github.com/oneapi-src/oneDNN#oneapi-deep-neural-network-library-onednn
 stdenv.mkDerivation (finalAttrs: {
  pname = "oneDNN";
-  version = "3.4";
+  version = "3.4.1";

  src = fetchFromGitHub {
    owner = "oneapi-src";
    repo = "oneDNN";
    rev = "v${finalAttrs.version}";
-    hash = "sha256-uV/Skp//tGy/hZBeN2NCbectlSoaz+H0ukYQd2j1lC4=";
+    hash = "sha256-6iPcytsRWvDn2hg5tkSG6A3cv/aOhmEVd5rS2uOKCPk=";
  };

  outputs = [ "out" "dev" "doc" ];
--- a/pkgs/development/python-modules/astropy/default.nix
+++ b/pkgs/development/python-modules/astropy/default.nix
@ -12,6 +12,7 @@
 , wheel
 # testing
 , pytestCheckHook
+, stdenv
 , pytest-xdist
 , pytest-astropy

@ -82,6 +83,9 @@ buildPythonPackage rec {
    # More flaky tests, see: https://github.com/NixOS/nixpkgs/issues/294392
    "test_sidereal_lon_independent"
    "test_timedelta_full_precision_arithmetic"
+    "test_datetime_to_timedelta"
+  ] ++ lib.optionals stdenv.isDarwin [
+    "test_sidereal_lat_independent"
  ];

  meta = {
--- a/pkgs/development/python-modules/dirigera/default.nix
+++ b/pkgs/development/python-modules/dirigera/default.nix
@ -1,17 +1,18 @@
-{ lib
-, buildPythonPackage
-, fetchFromGitHub
-, pydantic
-, pytestCheckHook
-, pythonOlder
-, requests
-, setuptools
-, websocket-client
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  pydantic,
+  pytestCheckHook,
+  pythonOlder,
+  requests,
+  setuptools,
+  websocket-client,
 }:

 buildPythonPackage rec {
  pname = "dirigera";
-  version = "1.0.12";
+  version = "1.0.14";
  pyproject = true;

  disabled = pythonOlder "3.7";
@ -20,12 +21,10 @@ buildPythonPackage rec {
    owner = "Leggin";
    repo = "dirigera";
    rev = "refs/tags/v${version}";
-    hash = "sha256-e8kbMP5ih7MBozFbylLEBR9DrS894X4xZh62OLLSgFw=";
+    hash = "sha256-FsW7ewKAvIONOjEXIOq7/GqOs564PpeMFKjS4crJtJ0=";
  };

-  build-system = [
-    setuptools
-  ];
+  build-system = [ setuptools ];

  dependencies = [
    pydantic
@ -33,13 +32,9 @@ buildPythonPackage rec {
    websocket-client
  ];

-  nativeCheckInputs = [
-    pytestCheckHook
-  ];
+  nativeCheckInputs = [ pytestCheckHook ];

-  pythonImportsCheck = [
-    "dirigera"
-  ];
+  pythonImportsCheck = [ "dirigera" ];

  meta = with lib; {
    description = "Module for controlling the IKEA Dirigera Smart Home Hub";
--- a/pkgs/development/python-modules/gfal2-python/default.nix
+++ b/pkgs/development/python-modules/gfal2-python/default.nix
@ -0,0 +1,53 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, cmake
+, pkg-config
+, boost
+, gfal2
+, glib
+, pythonAtLeast
+  # For tests
+, gfal2-util ? null
+}:
+buildPythonPackage rec {
+  pname = "gfal2-python";
+  version = "1.12.2";
+  src = fetchFromGitHub {
+    owner = "cern-fts";
+    repo = "gfal2-python";
+    rev = "v${version}";
+    hash = "sha256-Xk+gLTrqfWb0kGB6QhnM62zAHVFb8rRAqCIBxn0V824=";
+  };
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+  ];
+  buildInputs = [
+    boost
+    gfal2
+    glib
+  ];
+  # We don't want setup.py to (re-)execute cmake in buildPhase
+  # Besides, this package is totally handled by CMake, which means no additional configuration is needed.
+  dontConfigure = true;
+  pythonImportsCheck = [
+    "gfal2"
+  ];
+  passthru = {
+    inherit gfal2;
+    tests = {
+      inherit gfal2-util;
+    }
+    // lib.optionalAttrs (gfal2-util != null) gfal2-util.tests or { };
+  };
+  meta = with lib; {
+    description = "Python binding for gfal2";
+    homepage = "https://github.com/cern-fts/gfal2-python";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ ShamrockLee ];
+    # It currently fails to build against Python 3.12 or later,
+    # complaining CMake faililng to find Python include path, library path and site package path.
+    broken = pythonAtLeast "3.12";
+  };
+}
--- a/pkgs/development/python-modules/gfal2-util/default.nix
+++ b/pkgs/development/python-modules/gfal2-util/default.nix
@ -0,0 +1,103 @@
+{ lib
+, buildPythonPackage
+, callPackage
+, fetchFromGitHub
+, runCommandLocal
+  # Build inputs
+, gfal2-python
+  # For tests
+, xrootd # pkgs.xrootd
+}:
+(buildPythonPackage rec {
+  pname = "gfal2-util";
+  version = "1.8.1";
+  src = fetchFromGitHub {
+    owner = "cern-fts";
+    repo = "gfal2-util";
+    rev = "v${version}";
+    hash = "sha256-3JbJgKD17aYkrB/aaww7IQU8fLFrTCh868KWlLPxmlk=";
+  };
+
+  # Replace the ad-hoc python executable finding
+  # and change the shebangs from `#!/bin/sh` to `#!/usr/bin/env python`
+  # for fixup phase to work correctly.
+  postPatch = ''
+    for script in src/gfal-*; do
+      patch "$script" ${./gfal-util-script.patch}
+    done
+  '';
+
+  propagatedBuildInputs = [
+    gfal2-python
+  ];
+
+  pythonImportsCheck = [
+    "gfal2_util"
+  ];
+
+  meta = with lib; {
+    description = "CLI for gfal2";
+    homepage = "https://github.com/cern-fts/gfal2-utils";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ ShamrockLee ];
+  };
+}).overrideAttrs (finalAttrs: previousAttrs: lib.recursiveUpdate previousAttrs {
+  passthru = {
+    inherit (gfal2-python) gfal2;
+
+    fetchGfal2 = lib.makeOverridable (callPackage ./fetchgfal2.nix { gfal2-util = finalAttrs.finalPackage; });
+
+    # With these functionality tests, it should be safe to merge version bumps once all the tests are passed.
+    tests =
+      let
+        # Use the the bin output hash of gfal2-util as version to ensure that
+        # the test gets rebuild everytime gfal2-util gets rebuild
+        versionFODTests = finalAttrs.version + "-" + lib.substring (lib.stringLength builtins.storeDir + 1) 32 "${self}";
+        self = finalAttrs.finalPackage;
+      in
+      lib.optionalAttrs gfal2-python.gfal2.enablePluginStatus.xrootd (
+        let
+          # Test against a real-world dataset from CERN Open Data
+          # borrowed from `xrootd.tests`.
+          urlTestFile = xrootd.tests.test-xrdcp.url;
+          hashTestFile = xrootd.tests.test-xrdcp.outputHash;
+          urlTestDir = dirOf urlTestFile;
+        in
+        {
+          test-copy-file-xrootd = finalAttrs.passthru.fetchGfal2 {
+            url = urlTestFile;
+            hash = hashTestFile;
+            extraGfalCopyFlags = [ "--verbose" ];
+            pname = "gfal2-util-test-copy-file-xrootd";
+            version = versionFODTests;
+            allowSubstitutes = false;
+          };
+
+          test-copy-dir-xrootd = finalAttrs.passthru.fetchGfal2 {
+            url = urlTestDir;
+            hash = "sha256-vOahIhvx1oE9sfkqANMGUvGeLHS737wyfYWo4rkvrxw=";
+            recursive = true;
+            extraGfalCopyFlags = [ "--verbose" ];
+            pname = "gfal2-util-test-copy-dir-xrootd";
+            version = versionFODTests;
+            allowSubstitutes = false;
+          };
+
+          test-ls-dir-xrootd = (runCommandLocal "test-gfal2-util-ls-dir-xrootd" { } ''
+            set -eu -o pipefail
+            gfal-ls "$url" | grep "$baseNameExpected" | tee "$out"
+          '').overrideAttrs (finalAttrs: previousAttrs: {
+            pname = previousAttrs.name;
+            version = versionFODTests;
+            name = "${finalAttrs.pname}-${finalAttrs.version}";
+            nativeBuildInputs = [ self ];
+            url = urlTestDir;
+            baseNameExpected = baseNameOf urlTestFile;
+            outputHashMode = "flat";
+            outputHashAlgo = "sha256";
+            outputHash = builtins.hashString finalAttrs.outputHashAlgo (finalAttrs.baseNameExpected + "\n");
+          });
+        }
+      );
+  };
+})
--- a/pkgs/development/python-modules/gfal2-util/fetchgfal2.nix
+++ b/pkgs/development/python-modules/gfal2-util/fetchgfal2.nix
@ -0,0 +1,48 @@
+{ lib
+, runCommandLocal
+, gfal2-util
+}:
+
+# `url` and `urls` should only be overriden via `<pkg>.override`, but not `<pkg>.overrideAttrs`.
+{ name ? ""
+, pname ? ""
+, version ? ""
+, urls ? [ ]
+, url ? if urls == [ ] then abort "Expect either non-empty `urls` or `url`" else lib.head urls
+, hash ? lib.fakeHash
+, recursive ? false
+, intermediateDestUrls ? [ ]
+, extraGfalCopyFlags ? [ ]
+, allowSubstitutes ? true
+}:
+
+(runCommandLocal name { } ''
+  for u in "''${urls[@]}"; do
+    gfal-copy "''${gfalCopyFlags[@]}" "$u" "''${intermediateDestUrls[@]}" "$out"
+    ret="$?"
+    (( ret )) && break
+  done
+  if (( ret )); then
+    echo "gfal-copy failed trying to download from any of the urls" >&2
+    exit "$ret"
+  fi
+'').overrideAttrs (finalAttrs: previousAttrs:
+{
+  __structuredAttrs = true;
+  inherit allowSubstitutes;
+  nativeBuildInputs = [ gfal2-util ];
+  outputHashAlgo = null;
+  outputHashMode = if finalAttrs.recursive then "recursive" else "flat";
+  outputHash = hash;
+  inherit url;
+  urls = if urls == [ ] then lib.singleton url else urls;
+  gfalCopyFlags = extraGfalCopyFlags
+  ++ lib.optional finalAttrs.recursive "--recursive"
+  ;
+  inherit recursive intermediateDestUrls;
+} // (if (pname != "" && version != "") then {
+  inherit pname version;
+  name = "${finalAttrs.pname}-${finalAttrs.version}";
+} else {
+  name = if (name != "") then name else (baseNameOf url);
+}))
--- a/pkgs/development/python-modules/gfal2-util/gfal-util-script.patch
+++ b/pkgs/development/python-modules/gfal2-util/gfal-util-script.patch
@ -0,0 +1,19 @@
+--- a/gfal-SCRIPT_NAME	2022-11-17 00:00:00.000000000 +0000
+++ b/gfal-SCRIPT_NAME	2022-11-17 00:00:00.000000000 +0000
+@@ -1,4 +1,4 @@
+-#!/bin/sh
+#!/usr/bin/env python3
+ # -*- coding: utf-8 -*-
+ #
+ # Copyright (c) 2022 CERN
+@@ -15,10 +15,2 @@
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+-
+-# Execute script content with first python interpreter found:
+-# * GFAL_PYTHONBIN environment variable
+-# * python on the PATH if import gfal2, gfal2_util succeeds
+-# * python3 on the PATH if import gfal2, gfal2_util succeeds
+-# * python2 on the PATH if import gfal2, gfal2_util succeeds
+-# * /usr/bin/python
+-"exec" "$(  check_interpreter() { unalias $1 2> /dev/null; unset $1; GFAL_PYTHONBIN=$(command -v $1); [ $GFAL_PYTHONBIN ] && $GFAL_PYTHONBIN -c 'import gfal2, gfal2_util' > /dev/null 2>&1 && { echo $GFAL_PYTHONBIN; unset GFAL_PYTHONBIN; }; }; [ $GFAL_PYTHONBIN ] && echo $GFAL_PYTHONBIN || check_interpreter python || check_interpreter python3 || check_interpreter python2 || echo /usr/bin/python )" "-u" "-Wignore" "$0" "$@"
--- a/pkgs/development/python-modules/hcloud/default.nix
+++ b/pkgs/development/python-modules/hcloud/default.nix
@ -12,14 +12,14 @@

 buildPythonPackage rec {
  pname = "hcloud";
-  version = "1.34.0";
+  version = "1.35.0";
  pyproject = true;

  disabled = pythonOlder "3.7";

  src = fetchPypi {
    inherit pname version;
-    hash = "sha256-8hwr0K+6nLgAVMhXb/08CS7HrlLYQ/SV0K8MWH/PQk0=";
+    hash = "sha256-sZSatje+UXt69r7Nv4QMR3IvlHHGuHDm813h72/Oo+M=";
  };

  build-system = [
--- a/pkgs/development/python-modules/py-serializable/default.nix
+++ b/pkgs/development/python-modules/py-serializable/default.nix
@ -1,17 +1,18 @@
-{ lib
-, buildPythonPackage
-, defusedxml
-, fetchFromGitHub
-, lxml
-, poetry-core
-, pytestCheckHook
-, pythonOlder
-, xmldiff
+{
+  lib,
+  buildPythonPackage,
+  defusedxml,
+  fetchFromGitHub,
+  lxml,
+  poetry-core,
+  pytestCheckHook,
+  pythonOlder,
+  xmldiff,
 }:

 buildPythonPackage rec {
  pname = "py-serializable";
-  version = "1.0.2";
+  version = "1.0.3";
  pyproject = true;

  disabled = pythonOlder "3.8";
@ -20,16 +21,12 @@ buildPythonPackage rec {
    owner = "madpah";
    repo = "serializable";
    rev = "refs/tags/v${version}";
-    hash = "sha256-RhipoPTewPaYwspTnywLr5FvFVUaFixfRQk6aUMvB4w=";
+    hash = "sha256-oVjb7/9RWvQd5L6xQBrspfblPzMaRvnZHDuojTuq+zE=";
  };

-  nativeBuildInputs = [
-    poetry-core
-  ];
+  build-system = [ poetry-core ];

-  propagatedBuildInputs = [
-    defusedxml
-  ];
+  dependencies = [ defusedxml ];

  nativeCheckInputs = [
    lxml
@ -37,9 +34,7 @@ buildPythonPackage rec {
    xmldiff
  ];

-  pythonImportsCheck = [
-    "serializable"
-  ];
+  pythonImportsCheck = [ "serializable" ];

  disabledTests = [
    # AssertionError: '<ns0[155 chars]itle>The Phoenix
@ -48,7 +43,7 @@ buildPythonPackage rec {
  ];

  meta = with lib; {
-    description = "Pythonic library to aid with serialisation and deserialisation to/from JSON and XML";
+    description = "Library to aid with serialisation and deserialisation to/from JSON and XML";
    homepage = "https://github.com/madpah/serializable";
    changelog = "https://github.com/madpah/serializable/blob/v${version}/CHANGELOG.md";
    license = licenses.asl20;
--- a/pkgs/development/r-modules/bioc-annotation-packages.nix
+++ b/pkgs/development/r-modules/bioc-annotation-packages.nix
@ -7,7 +7,7 @@
 let derive2 = derive { biocVersion = "3.18"; };
 in with self; {
  AHCytoBands = derive2 { name="AHCytoBands"; version="0.99.1"; sha256="0svxxhj3mh5gqik45ikcxnlhnma8n1c0rv8pycj2034cb9ms1dbv"; depends=[]; };
-  AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.1.10"; sha256="0mqginwp70rwsmqwdl64awj4jr78n17rbaxmik86sk4n98fgd4xf"; depends=[AnnotationHubData ensembldb]; };
+  AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.1.11"; sha256="1mh8aji48a6fad6bd1333qmc3dw7b5hf4v7xw0zhmfbnld64gz0s"; depends=[AnnotationHubData ensembldb]; };
  AHLRBaseDbs = derive2 { name="AHLRBaseDbs"; version="1.7.0"; sha256="1nbgqv1c3nyhlniqvqdc5cf8kyys323z1ia5jw54hxwi1jdyclfg"; depends=[AnnotationHub]; };
  AHMeSHDbs = derive2 { name="AHMeSHDbs"; version="1.7.0"; sha256="0hxik2xzvbgv6a936mvax5kyv65drr36r9rf7rlv124jinlbxw82"; depends=[AnnotationHub]; };
  AHPathbankDbs = derive2 { name="AHPathbankDbs"; version="0.99.5"; sha256="10wcrglm521xcrfbzc39dkbjvg1pkz0zq70vgnh68akiwmdirp89"; depends=[AnnotationHub]; };
@ -348,7 +348,7 @@ in with self; {
  excluderanges = derive2 { name="excluderanges"; version="0.99.8"; sha256="19pdwlhqlz420yss371bsqhkx8c7wxr0sv4wsycnc0mlplwq4bsf"; depends=[GenomicRanges]; };
  fitCons_UCSC_hg19 = derive2 { name="fitCons.UCSC.hg19"; version="3.7.1"; sha256="19isa4x8js0pdb4k8a11bw3bzmzv6jc4jphzrvav7piqkvrgykzx"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; };
  fly_db0 = derive2 { name="fly.db0"; version="3.18.0"; sha256="1pksr9jwdd5izf2yc7fb935pic84nvlxa458h0da9lryglc0w5rg"; depends=[AnnotationDbi]; };
-  geneplast_data = derive2 { name="geneplast.data"; version="0.99.8"; sha256="1dd7jbgr1binab11npc4qk6caa4n3hzcfdjbsi56f0xic73f8w1b"; depends=[ape BiocFileCache dplyr geneplast igraph purrr readr tibble treeio]; };
+  geneplast_data = derive2 { name="geneplast.data"; version="0.99.9"; sha256="1i31kx4kckfg965s9l3pilvmg847av3rpa05aql43259ccyng4hi"; depends=[ape BiocFileCache dplyr geneplast igraph purrr readr tibble tidyr treeio]; };
  geneplast_data_string_v91 = derive2 { name="geneplast.data.string.v91"; version="0.99.6"; sha256="0mc26d0sgmpmfmqsqinqv5k6vhg0hlc8hsjkcnvf369yav224nq1"; depends=[]; };
  genomewidesnp5Crlmm = derive2 { name="genomewidesnp5Crlmm"; version="1.0.6"; sha256="06dmwnjy3gb53y6nr02dmp22qzfl5d63wppazrabcqbzwimhnvp8"; depends=[]; };
  genomewidesnp6Crlmm = derive2 { name="genomewidesnp6Crlmm"; version="1.0.7"; sha256="16qcxa32fmbdcv5dck0grsnqyfcqql7wpxa1l6andv9hrvabv2jx"; depends=[]; };
--- a/pkgs/development/r-modules/bioc-experiment-packages.nix
+++ b/pkgs/development/r-modules/bioc-experiment-packages.nix
@ -43,10 +43,10 @@ in with self; {
  ConnectivityMap = derive2 { name="ConnectivityMap"; version="1.38.0"; sha256="0ixvmkyps62f10c0s4z0jas2106hnvijknai6abial6i3plffnsc"; depends=[]; };
  CopyNeutralIMA = derive2 { name="CopyNeutralIMA"; version="1.20.0"; sha256="11l994nhi813qs1vmrqjgclw11k5hrsmcrlj5x5wqmqmnjjw1dsy"; depends=[ExperimentHub Rdpack]; };
  CopyhelpeR = derive2 { name="CopyhelpeR"; version="1.34.0"; sha256="1zfsxi65lln93fb87l6fgp7vxldb4fvnf95h91dl424xyq6qjp1h"; depends=[]; };
-  DAPARdata = derive2 { name="DAPARdata"; version="1.32.0"; sha256="1bf8sv9fpp9mpyb5r83a6r2b92d5nc0gwiys2avd0nlmzjddj4jw"; depends=[MSnbase]; };
+  DAPARdata = derive2 { name="DAPARdata"; version="1.32.1"; sha256="1iwiq5z1jnsrdp3pnhxlb2rvcfg91xp7xp2k0ry7r0gr9hjnnhr7"; depends=[MSnbase]; };
  DExMAdata = derive2 { name="DExMAdata"; version="1.10.0"; sha256="1a2hrvbkhpwmjha0iwd17xv60d1cdl7iswc942bcac80mn6sw305"; depends=[Biobase]; };
-  DLBCL = derive2 { name="DLBCL"; version="1.42.1"; sha256="0an4g45977knk2qsvwjjm66l7rrb26pbk8sbb1zjvmrqym1qviqj"; depends=[Biobase graph]; };
-  DMRcatedata = derive2 { name="DMRcatedata"; version="2.20.0"; sha256="07gkhal6rhj9b4yasmb3dfix38cd99p2bf79agl8vbrmzd0mjvhc"; depends=[ExperimentHub GenomicFeatures Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 plyr readxl rtracklayer]; };
+  DLBCL = derive2 { name="DLBCL"; version="1.42.2"; sha256="06x4jbyz0m9pzwxjl326rl5zahq5km5rryncbq99cz6mml2asn21"; depends=[Biobase graph]; };
+  DMRcatedata = derive2 { name="DMRcatedata"; version="2.20.3"; sha256="0fhk71j60s693vh333277ra0vgjys15h6r593v2j1y970650pq0a"; depends=[ExperimentHub GenomicFeatures Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 plyr readxl rtracklayer]; };
  DNAZooData = derive2 { name="DNAZooData"; version="1.2.0"; sha256="0d5466b830s82laamig1rw0p0n6i4npb11iyziv1sfvs4y8pbhl8"; depends=[BiocFileCache HiCExperiment rjson S4Vectors]; };
  DeSousa2013 = derive2 { name="DeSousa2013"; version="1.38.0"; sha256="1xjygkr8rc1m9sv5bwph3wdf9hhcfdw8zji547nw0ayrg5d49689"; depends=[affy AnnotationDbi Biobase cluster ConsensusClusterPlus frma frmaTools gplots hgu133plus2_db hgu133plus2frmavecs pamr rgl ROCR siggenes survival sva]; };
  DmelSGI = derive2 { name="DmelSGI"; version="1.34.0"; sha256="1qsvw7jrn070yfrgrkw9wsdb05g8ai5hmcqmyr78qs5qny0cz919"; depends=[abind gplots igraph knitr limma rhdf5 TSP]; };
@ -83,7 +83,7 @@ in with self; {
  HCAData = derive2 { name="HCAData"; version="1.18.0"; sha256="1rd1qra8g7dn9pg2mhh2j40p7p6ny838n4w6mx5ryw4xky95lf41"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; };
  HCATonsilData = derive2 { name="HCATonsilData"; version="1.0.0"; sha256="1h5hrfslhyiqc855bb23rz9hahnpcy47h2lz1k0dj8glrjldq0jp"; depends=[base64enc ExperimentHub HDF5Array htmltools rmarkdown S4Vectors SingleCellExperiment SpatialExperiment SummarizedExperiment]; };
  HD2013SGI = derive2 { name="HD2013SGI"; version="1.42.0"; sha256="1xxc85al19qxj17rj1k4q0xp3wgkxr007akmq3an7mqrah0y8hm8"; depends=[EBImage geneplotter gplots limma LSD RColorBrewer splots vcd]; };
-  HDCytoData = derive2 { name="HDCytoData"; version="1.22.0"; sha256="1xqwkwxaaj5yylx9pzvka8pj9gxg1z4g23d2sralcvqzcz7q13zn"; depends=[ExperimentHub flowCore SummarizedExperiment]; };
+  HDCytoData = derive2 { name="HDCytoData"; version="1.22.1"; sha256="1048xgypsw257ihy0ysfxy5443dzhzp2rkjjvpivvrhw4dzl25ir"; depends=[ExperimentHub flowCore SummarizedExperiment]; };
  HEEBOdata = derive2 { name="HEEBOdata"; version="1.40.0"; sha256="1xijrm32p191qydz1gkm8321b8ycb9h6y6m1qvc8shlhbbzw705h"; depends=[]; };
  HIVcDNAvantWout03 = derive2 { name="HIVcDNAvantWout03"; version="1.42.0"; sha256="0kyblhc6fdc5c45qyqcr2qnmp1zrwdrc0j91fml04pw5yxrf6dw0"; depends=[]; };
  HMP16SData = derive2 { name="HMP16SData"; version="1.22.0"; sha256="1ns7yyw0w8rrkw87awrrzxmb44gkkb1cn6j3cbzj8fbrd9whl30d"; depends=[AnnotationHub assertthat dplyr ExperimentHub kableExtra knitr magrittr readr S4Vectors stringr SummarizedExperiment tibble]; };
@ -192,7 +192,7 @@ in with self; {
  SNAData = derive2 { name="SNAData"; version="1.48.0"; sha256="0qd48ggg1wjy5h47hzl9iqzy13gsxxn4f7fq4b0ra35vhckmcvyf"; depends=[graph]; };
  SNAGEEdata = derive2 { name="SNAGEEdata"; version="1.38.0"; sha256="17wbf4xsljkryzjpk57kvjbiln0ig8d717j953wy0inz7vzdkpkn"; depends=[]; };
  SNPhoodData = derive2 { name="SNPhoodData"; version="1.32.0"; sha256="0p8361lmlfz496ivw9qaqkg7b3hr4gb9g9r73fxp6amy2xncb00g"; depends=[]; };
-  STexampleData = derive2 { name="STexampleData"; version="1.10.0"; sha256="1rhq1743aa9bw54d2c74yclwd56a5vq5jppfzxz7mmv3cf5x3ar9"; depends=[ExperimentHub SpatialExperiment]; };
+  STexampleData = derive2 { name="STexampleData"; version="1.10.1"; sha256="1fr29mnczvglpkwh4vdy6klahv014ikmxwx055x4grkxvygbqm23"; depends=[ExperimentHub SpatialExperiment]; };
  SVM2CRMdata = derive2 { name="SVM2CRMdata"; version="1.34.0"; sha256="1k7cjakxcqq86xvx0d0799hb94hi7w05amd9yncd0nf4dcy6zm0f"; depends=[]; };
  SimBenchData = derive2 { name="SimBenchData"; version="1.10.0"; sha256="1g5wff2hx3sra48wcvwh3hs9lpfavq2pqflcm9wfcch9y10m8iqd"; depends=[ExperimentHub S4Vectors]; };
  Single_mTEC_Transcriptomes = derive2 { name="Single.mTEC.Transcriptomes"; version="1.30.0"; sha256="1w3f71mfq74sjlsasi87gvqs2mhny41zm22zswz9km5msi8r2wva"; depends=[]; };
@ -224,7 +224,7 @@ in with self; {
  VectraPolarisData = derive2 { name="VectraPolarisData"; version="1.6.0"; sha256="0zr94qgyj365sy7cyzjsm9zbxyv6zbd8lwfr1nqz0p6f6hb9b8qw"; depends=[ExperimentHub SpatialExperiment]; };
  WES_1KG_WUGSC = derive2 { name="WES.1KG.WUGSC"; version="1.34.0"; sha256="1p8z4p1s5l4hlp78ifiy3gan1n8iljaafbqv88vxwbjh2x9gfnjl"; depends=[]; };
  WGSmapp = derive2 { name="WGSmapp"; version="1.14.0"; sha256="0yv323mkv681f20dzjh1xaz19xbn4j777xxlmq27rvmk3j1vfah9"; depends=[GenomicRanges]; };
-  WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.4.0"; sha256="1r6an1lxjsrdi4y0prfyy9jjjazicy9bwykinf5dvkac2h3zhs81"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
+  WeberDivechaLCdata = derive2 { name="WeberDivechaLCdata"; version="1.4.1"; sha256="00ws47shsfnwi6c3ah56bm6dvicfhfr50jadll613fddv7cxkfsw"; depends=[ExperimentHub SingleCellExperiment SpatialExperiment]; };
  XhybCasneuf = derive2 { name="XhybCasneuf"; version="1.40.0"; sha256="1qzbsmqn9y1483108pzh8zkiw1q1xzghincrcmz8cl2a4q10hyxf"; depends=[affy ath1121501cdf RColorBrewer tinesath1cdf]; };
  adductData = derive2 { name="adductData"; version="1.18.0"; sha256="16c79wy55p4ryglxph80dibfm1ni8c5yfk6fnmq064ihw4zwcld5"; depends=[AnnotationHub ExperimentHub]; };
  affycompData = derive2 { name="affycompData"; version="1.40.0"; sha256="183wgbc4j7f9d4rwr9smndnmw1i390abak23wp6p02zk340qmvq4"; depends=[affycomp Biobase]; };
@ -274,13 +274,13 @@ in with self; {
  curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="3.10.0"; sha256="0fgvpxc1878lm8l0bib12zzwrgsap0vw4zn77qpz1mljnz43shcb"; depends=[AnnotationHub dplyr ExperimentHub magrittr mia purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect TreeSummarizedExperiment]; };
  curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.40.1"; sha256="18163l0g3g042m2qgz143smxia3lp8v7rddkqmkg4hzns7baxfaa"; depends=[Biobase BiocGenerics]; };
  curatedTBData = derive2 { name="curatedTBData"; version="1.8.0"; sha256="116ck61pw6diili326x0x8p7f8d5w624n4w3pd212vhq8555yrqs"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment rlang]; };
-  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.24.0"; sha256="0kfdzc5arzsrdaps7b3r718yawpv1x7wms5jp90j8cxpn0hz07az"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
+  curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.24.1"; sha256="0hr66p8l54nzfsizcxxd2njy44xnia607wvfhrgv46f3f8s95z02"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; };
  davidTiling = derive2 { name="davidTiling"; version="1.42.0"; sha256="1xfkyncwi9zrynk6dqsmacmkxx2qvj1axda3wn55b1vbw2wimpyf"; depends=[Biobase GO_db tilingArray]; };
  depmap = derive2 { name="depmap"; version="1.16.0"; sha256="1vb3f5ar2jlkjyhp7rv4imlylinm6fi94ki277jgdaxn12v78qxj"; depends=[AnnotationHub dplyr ExperimentHub]; };
  derfinderData = derive2 { name="derfinderData"; version="2.20.0"; sha256="1h8rl8mnxk2lsl8xa8mihvbd77yw32fpxdbhhn4rv1v8i5j35r7l"; depends=[]; };
  diffloopdata = derive2 { name="diffloopdata"; version="1.30.0"; sha256="1f0gnwpjxkby7kd2bphnz4lv7gx9k297yqz0b954m7adp1sh6aqa"; depends=[]; };
  diggitdata = derive2 { name="diggitdata"; version="1.34.0"; sha256="01r356zdy4pi8z90pbww8q7dfmq09zf148d5sq3w22z1ypsy6zm1"; depends=[Biobase viper]; };
-  dorothea = derive2 { name="dorothea"; version="1.14.0"; sha256="1vinixcpl4hjjfw48qfngsvw1yr82yscdxrsgagdm8gm7b72qjgh"; depends=[bcellViper decoupleR dplyr magrittr]; };
+  dorothea = derive2 { name="dorothea"; version="1.14.1"; sha256="0bjmnqly57y69axnz5q2rqz7j7dnz1xzbhbzcalv99kybjiyqyb5"; depends=[bcellViper decoupleR dplyr magrittr]; };
  dressCheck = derive2 { name="dressCheck"; version="0.40.0"; sha256="1mb6cmyf61rb7jdwczhzcvadgqijij53w03d87xq7zqsc7jxi9z3"; depends=[Biobase]; };
  dyebiasexamples = derive2 { name="dyebiasexamples"; version="1.42.0"; sha256="06sp4fxsph3w84g960s65sy1vc032p2xj3sf0v94nh78f6myg0mj"; depends=[GEOquery marray]; };
  easierData = derive2 { name="easierData"; version="1.8.0"; sha256="138x8i1zd4cvlawg9pa5ia1kmmdaxm0g9lkivzxl077s9vlpjp8d"; depends=[AnnotationHub ExperimentHub SummarizedExperiment]; };
--- a/pkgs/development/r-modules/bioc-packages.nix
+++ b/pkgs/development/r-modules/bioc-packages.nix
--- a/pkgs/development/r-modules/cran-packages.nix
+++ b/pkgs/development/r-modules/cran-packages.nix
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@ -304,8 +304,10 @@ let
  };

  packagesWithRDepends = {
+    spectralGraphTopology = [ self.CVXR ];
    FactoMineR = [ self.car ];
    pander = [ self.codetools ];
+    rmsb = [ self.rstantools ];
  };

  packagesWithNativeBuildInputs = {
@ -359,11 +361,11 @@ let
    HiCseg = [ pkgs.gsl ];
    imager = [ pkgs.xorg.libX11.dev ];
    iBMQ = [ pkgs.gsl ];
-    igraph = with pkgs; [ gmp libxml2.dev ];
    JavaGD = [ pkgs.jdk ];
    jpeg = [ pkgs.libjpeg.dev ];
    jqr = [ pkgs.jq.dev ];
    KFKSDS = [ pkgs.gsl ];
+    KSgeneral = with pkgs; [ pkg-config ];
    kza = [ pkgs.fftw.dev ];
    leidenAlg = [ pkgs.gmp.dev ];
    Libra = [ pkgs.gsl ];
@ -404,6 +406,7 @@ let
    RcppZiggurat = [ pkgs.gsl ];
    reprex = [ pkgs.which ];
    rgdal = with pkgs; [ proj.dev gdal ];
+    gdalcubes = [ pkgs.pkg-config ];
    rgeos = [ pkgs.geos ];
    Rglpk = [ pkgs.glpk ];
    RGtk2 = [ pkgs.gtk2.dev ];
@ -443,6 +446,7 @@ let
    seqminer = with pkgs; [ zlib.dev bzip2 ];
    sf = with pkgs; [ gdal proj geos libtiff curl ];
    strawr = with pkgs; [ curl.dev ];
+    string2path = [ pkgs.cargo ];
    terra = with pkgs; [ gdal proj geos ];
    apcf = with pkgs; [ geos ];
    SemiCompRisks = [ pkgs.gsl ];
@ -464,6 +468,7 @@ let
    topicmodels = [ pkgs.gsl ];
    udunits2 = with pkgs; [ udunits expat ];
    units = [ pkgs.udunits ];
+    unigd = [ pkgs.pkg-config ];
    vdiffr = [ pkgs.libpng.dev ];
    V8 = [ pkgs.v8 ];
    XBRL = with pkgs; [ zlib libxml2.dev ];
@ -471,21 +476,18 @@ let
    xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
    XML = with pkgs; [ libtool libxml2.dev xmlsec libxslt ];
    affyPLM = [ pkgs.zlib.dev ];
-    bamsignals = [ pkgs.zlib.dev ];
    BitSeq = [ pkgs.zlib.dev ];
-    DiffBind = [ pkgs.zlib ];
+    DiffBind = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
    ShortRead = [ pkgs.zlib.dev ];
    oligo = [ pkgs.zlib.dev ];
    gmapR = [ pkgs.zlib.dev ];
    Rsubread = [ pkgs.zlib.dev ];
    XVector = [ pkgs.zlib.dev ];
-    Rsamtools = with pkgs; [ zlib.dev curl.dev ];
+    Rsamtools = with pkgs; [ zlib.dev curl.dev bzip2 xz ];
    rtracklayer = [ pkgs.zlib.dev ];
    affyio = [ pkgs.zlib.dev ];
-    VariantAnnotation = with pkgs; [ zlib.dev curl.dev ];
    snpStats = [ pkgs.zlib.dev ];
    vcfppR = [ pkgs.curl.dev pkgs.bzip2 pkgs.zlib.dev pkgs.xz];
-    hdf5r = [ pkgs.hdf5.dev ];
    httpgd = with pkgs; [ cairo.dev ];
    SymTS = [ pkgs.gsl ];
    VBLPCM = [ pkgs.gsl ];
@ -516,6 +518,7 @@ let
    RationalMatrix = [ pkgs.pkg-config pkgs.gmp.dev];
    RcppCWB = [ pkgs.pkg-config pkgs.pcre2 ];
    redux = [ pkgs.pkg-config ];
+    rswipl = with pkgs; [ cmake pkg-config ];
    rrd = [ pkgs.pkg-config ];
    Rbwa = [ pkgs.zlib.dev ];
    trackViewer = [ pkgs.zlib.dev ];
@ -562,9 +565,13 @@ let
    fftw = [ pkgs.pkg-config ];
    gdtools = [ pkgs.pkg-config ];
    archive = [ pkgs.libarchive];
+    gdalcubes = with pkgs; [ proj.dev gdal sqlite.dev netcdf ];
    SuperGauss = [ pkgs.pkg-config pkgs.fftw.dev];
+    cartogramR = [ pkgs.fftw.dev ];
    jqr = [ pkgs.jq.lib ];
    kza = [ pkgs.pkg-config ];
+    igraph = with pkgs; [ gmp libxml2.dev glpk ];
+    image_textlinedetector = with pkgs; [ pkg-config opencv ];
    lwgeom = with pkgs; [ pkg-config proj.dev sqlite.dev ];
    magick = [ pkgs.pkg-config ];
    mwaved = [ pkgs.pkg-config ];
@ -583,11 +590,13 @@ let
    CLVTools = [ pkgs.gsl ];
    excursions = [ pkgs.gsl ];
    JMcmprsk = [ pkgs.gsl ];
+    KSgeneral = [ pkgs.fftw.dev ];
    mashr = [ pkgs.gsl ];
    hadron = [ pkgs.gsl ];
    AMOUNTAIN = [ pkgs.gsl ];
    Rsymphony = with pkgs; [ pkg-config doxygen graphviz subversion ];
    tcltk2 = with pkgs; [ tcl tk ];
+    rswipl = with pkgs; [ ncurses.dev libxcrypt zlib.dev ];
    tikzDevice = with pkgs; [ which texliveMedium ];
    gridGraphics = [ pkgs.which ];
    adimpro = with pkgs; [ which xorg.xdpyinfo ];
@ -603,9 +612,10 @@ let
    bio3d = with pkgs; [ zlib.dev ];
    arrangements = with pkgs; [ gmp.dev ];
    spp = with pkgs; [ zlib.dev ];
+    bamsignals = with pkgs; [ zlib.dev xz.dev bzip2 ];
    Rbowtie = with pkgs; [ zlib.dev ];
    gaston = with pkgs; [ zlib.dev ];
-    csaw = with pkgs; [ zlib.dev curl ];
+    csaw = with pkgs; [ zlib.dev xz.dev bzip2.dev curl ];
    DirichletMultinomial = with pkgs; [ gsl ];
    DiffBind = with pkgs; [ zlib.dev ];
    CNEr = with pkgs; [ zlib ];
@ -613,8 +623,9 @@ let
    rmumps = with pkgs; [ zlib.dev ];
    HiCDCPlus = [ pkgs.zlib.dev ];
    PopGenome = [ pkgs.zlib.dev ];
-    QuasR = [ pkgs.zlib.dev ];
+    QuasR = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
    Rbowtie2 = [ pkgs.zlib.dev ];
+    maftools = with pkgs; [ zlib.dev bzip2 xz.dev ];
    Rmmquant = [ pkgs.zlib.dev ];
    SICtools = with pkgs; [ zlib.dev ncurses.dev ];
    Signac = [ pkgs.zlib.dev ];
@ -623,11 +634,12 @@ let
    zlib = [ pkgs.zlib.dev ];
    divest = [ pkgs.zlib.dev ];
    hipread = [ pkgs.zlib.dev ];
-    jackalope = with pkgs; [ zlib.dev xz.dev ];
+    jackalope = with pkgs; [ zlib.dev xz.dev bzip2.dev ];
    largeList = [ pkgs.zlib.dev ];
    mappoly = [ pkgs.zlib.dev ];
+    VariantAnnotation = with pkgs; [ zlib.dev curl.dev bzip2.dev xz.dev ];
    matchingMarkets = [ pkgs.zlib.dev ];
-    methylKit = [ pkgs.zlib.dev ];
+    methylKit = with pkgs; [ zlib.dev bzip2.dev xz.dev ];
    ndjson = [ pkgs.zlib.dev ];
    podkat = [ pkgs.zlib.dev ];
    qrqc = [ pkgs.zlib.dev ];
@ -640,6 +652,7 @@ let
    seqbias = [ pkgs.zlib.dev ];
    sparkwarc = [ pkgs.zlib.dev ];
    RoBMA = [ pkgs.jags ];
+    pexm = [ pkgs.jags ];
    rGEDI = with pkgs; [ libgeotiff.dev libaec zlib.dev hdf5.dev ];
    rawrr = [ pkgs.mono ];
    HDF5Array = [ pkgs.zlib.dev ];
@ -674,12 +687,13 @@ let
    RcppAlgos = [ pkgs.gmp.dev ];
    RcppBigIntAlgos = [ pkgs.gmp.dev ];
    spaMM = [ pkgs.gsl ];
+    unigd = with pkgs; [ cairo.dev libpng.dev ];
    HilbertVisGUI = [ pkgs.gtkmm2.dev ];
    textshaping = with pkgs; [ harfbuzz.dev freetype.dev fribidi libpng ];
    DropletUtils = [ pkgs.zlib.dev ];
    RMariaDB = [ pkgs.libmysqlclient.dev ];
    ijtiff = [ pkgs.libtiff ];
-    ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ];
+    ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ] ++ lib.optional stdenv.isDarwin lerc.dev;
    qqconf = [ pkgs.fftw.dev ];
    vapour = with pkgs; [ proj.dev gdal ];
  };
@ -882,12 +896,14 @@ let
    "aroma_affymetrix"
    "aroma_cn"
    "aroma_core"
+    "connections"
    "csodata"
    "DiceView"
    "MSnID"
    "OmnipathR"
    "precommit"
    "PSCBS"
+    "iemisc"
    "repmis"
    "R_cache"
    "R_filesets"
@ -1054,6 +1070,29 @@ let
      patchPhase = "patchShebangs configure";
    });

+    exifr = old.exifr.overrideAttrs (attrs: {
+      postPatch = ''
+        for f in .onLoad .onAttach ; do
+          substituteInPlace R/load_hook.R \
+            --replace-fail \
+            "$f <- function(libname, pkgname) {" \
+            "$f <- function(libname, pkgname) {
+                 options(
+                     exifr.perlpath = \"${lib.getBin pkgs.perl}/bin/perl\",
+                     exifr.exiftoolcommand = \"${lib.getBin pkgs.exiftool}/bin/exiftool\"
+                 )"
+        done
+      '';
+    });
+
+    NGCHM = old.NGCHM.overrideAttrs (attrs: {
+      postPatch = ''
+          substituteInPlace "inst/base.config/conf.d/01-server-protocol-scl.R" \
+            --replace-fail \
+            "/bin/hostname" "${lib.getBin pkgs.hostname}/bin/hostname"
+      '';
+    });
+
    ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: {
      env = (attrs.env or { }) // {
        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.isDarwin " -fopenmp";
@ -1151,6 +1190,10 @@ let
      NIX_LDFLAGS = "-lX11";
    });

+    hdf5r = old.hdf5r.overrideAttrs (attrs: {
+      buildInputs = attrs.buildInputs ++ [ new.Rhdf5lib.hdf5 ];
+    });
+
    slfm = old.slfm.overrideAttrs (attrs: {
      PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
    });
@ -1183,6 +1226,10 @@ let
      ];
    });

+    universalmotif = old.universalmotif.overrideAttrs (attrs: {
+      patches = [ ./patches/universalmotif.patch];
+    });
+
    V8 = old.V8.overrideAttrs (attrs: {
      postPatch = ''
        substituteInPlace configure \
@ -1417,6 +1464,10 @@ let

    flowClust = old.flowClust.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };

+    RcppCGAL = old.RcppCGAL.overrideAttrs (_: {
+      postPatch = "patchShebangs configure";
+    });
+
    httr2 = old.httr2.overrideAttrs (attrs: {
      preConfigure = "patchShebangs configure";
    });
@ -1433,7 +1484,7 @@ let
    });

    Rhdf5lib = let
-      hdf5 = pkgs.hdf5_1_10.overrideAttrs (attrs: {configureFlags = attrs.configureFlags ++ ["--enable-cxx"];});
+      hdf5 = pkgs.hdf5_1_10.overrideAttrs (attrs: {configureFlags = attrs.configureFlags ++ [ "--enable-cxx" ];});
    in old.Rhdf5lib.overrideAttrs (attrs: {
      propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ hdf5.dev pkgs.libaec ];
      patches = [ ./patches/Rhdf5lib.patch ];
@ -1497,6 +1548,12 @@ let
        patchShebangs src/library/ps/configure
      '';
    });
+
+    pkgdepends = old.pkgdepends.overrideAttrs (attrs: {
+      postPatch = ''
+        patchShebangs configure
+      '';
+    });
  };
 in
  self
--- a/pkgs/development/r-modules/patches/universalmotif.patch
+++ b/pkgs/development/r-modules/patches/universalmotif.patch
@ -0,0 +1,10 @@
+diff --git a/src/Makevars b/src/Makevars
+index 6e08950..e66fbbd 100644
+--- a/src/Makevars
+++ b/src/Makevars
+@@ -1,5 +1 @@
+ CXX_STD=CXX11
+-PKG_LIBS=`"$(R_HOME)/bin/Rscript" -e "RcppThread::LdFlags()"`
+-strippedLib: $(SHLIB)
+-		if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
+-.phony: strippedLib
--- a/pkgs/development/tools/azure-static-sites-client/versions.json
+++ b/pkgs/development/tools/azure-static-sites-client/versions.json
@ -1,25 +1,44 @@
 [
  {
    "version": "latest",
-    "buildId": "1.0.026164",
-    "publishDate": "2024-02-29T20:38:30.619614Z",
+    "buildId": "1.0.026361",
+    "publishDate": "2024-03-20T18:04:43.3376902Z",
    "files": {
      "linux-x64": {
-        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026164/linux/StaticSitesClient",
-        "sha": "7b2d674a63fb0cb1ee39b84348260755c872a2922d03c0ee55eea1c8eb385524"
+        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026361/linux/StaticSitesClient",
+        "sha": "e7430ccd96669bbb91204affa5bc313dc6af1f848d704dd7dacf9a2927b3d130"
      },
      "win-x64": {
-        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026164/windows/StaticSitesClient.exe",
-        "sha": "57f8db0e48c772f4eadd9cbab1996354ecdf193f0d123df02dfa4a7eb6398a15"
+        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026361/windows/StaticSitesClient.exe",
+        "sha": "f3e2e686f742029a7b641e7cc6d3727398fbe783505df8cf75c334da980d2cd4"
      },
      "osx-x64": {
-        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026164/macOS/StaticSitesClient",
-        "sha": "fd0e8fe34ba0776c1fc44a8e66017b3abe33b044f429a95e6863919e920bf555"
+        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026361/macOS/StaticSitesClient",
+        "sha": "85bc201ed956ec41bc0a730dc5652c3c8bded946ebcf1c1ff31350490118a324"
      }
    }
  },
  {
    "version": "stable",
+    "buildId": "1.0.026361",
+    "publishDate": "2024-03-20T18:04:43.3376902Z",
+    "files": {
+      "linux-x64": {
+        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026361/linux/StaticSitesClient",
+        "sha": "e7430ccd96669bbb91204affa5bc313dc6af1f848d704dd7dacf9a2927b3d130"
+      },
+      "win-x64": {
+        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026361/windows/StaticSitesClient.exe",
+        "sha": "f3e2e686f742029a7b641e7cc6d3727398fbe783505df8cf75c334da980d2cd4"
+      },
+      "osx-x64": {
+        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.026361/macOS/StaticSitesClient",
+        "sha": "85bc201ed956ec41bc0a730dc5652c3c8bded946ebcf1c1ff31350490118a324"
+      }
+    }
+  },
+  {
+    "version": "backup",
    "buildId": "1.0.026164",
    "publishDate": "2024-02-29T20:38:30.619614Z",
    "files": {
@ -36,24 +55,5 @@
        "sha": "fd0e8fe34ba0776c1fc44a8e66017b3abe33b044f429a95e6863919e920bf555"
      }
    }
-  },
-  {
-    "version": "backup",
-    "buildId": "1.0.025891",
-    "publishDate": "2024-02-02T19:23:37.1915908Z",
-    "files": {
-      "linux-x64": {
-        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.025891/linux/StaticSitesClient",
-        "sha": "798b4032d1b6cd3f7057a6b7510c502dd69fa8cb4d27d47433542e8e80e9f87c"
-      },
-      "win-x64": {
-        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.025891/windows/StaticSitesClient.exe",
-        "sha": "097f9633c12b55e85e4ea9c053576a94b4f5847ce3a5a7671112c881878cfc4b"
-      },
-      "osx-x64": {
-        "url": "https://swalocaldeploy.azureedge.net/downloads/1.0.025891/macOS/StaticSitesClient",
-        "sha": "142310370774f91526c5d08ebde2f0b224b4f7f88bb6e514d25c1ef6f04fd8c8"
-      }
-    }
  }
 ]
--- a/pkgs/development/tools/continuous-integration/cirrus-cli/default.nix
+++ b/pkgs/development/tools/continuous-integration/cirrus-cli/default.nix
@ -6,16 +6,16 @@

 buildGoModule rec {
  pname = "cirrus-cli";
-  version = "0.113.1";
+  version = "0.114.2";

  src = fetchFromGitHub {
    owner = "cirruslabs";
    repo = pname;
    rev = "v${version}";
-    sha256 = "sha256-RAka5uYNsTq/zBT9sjdrZFY1CmJ5Vzdj1gfWvMERcPA=";
+    sha256 = "sha256-msWvi2aUrGLfTCkBuKt9LQA3Dui74Pw3l1YHT0RPinw=";
  };

-  vendorHash = "sha256-NPtQM4nm8QiHY2wSd7VHx6T5LRb7EB39x+xFzHOUcNs=";
+  vendorHash = "sha256-f/OIgQBneXdEL2cfTvNK2kLMb8Ag9hqhhD0bXwaY/hM=";

  ldflags = [
    "-X github.com/cirruslabs/cirrus-cli/internal/version.Version=v${version}"
--- a/pkgs/development/tools/gci/default.nix
+++ b/pkgs/development/tools/gci/default.nix
@ -5,13 +5,13 @@
 }:
 buildGoModule rec {
  pname = "gci";
-  version = "0.13.2";
+  version = "0.13.4";

  src = fetchFromGitHub {
    owner = "daixiang0";
    repo = pname;
    rev = "v${version}";
-    sha256 = "sha256-Wh6vkyfubgEHKjGjaICktRZiCYy8Cn1zMQMrQWEqQ/k=";
+    sha256 = "sha256-nJyRgvMVmNmmxigsdDcKzUuTQg5lXa8JnmwVyQwyWxA=";
  };

  vendorHash = "sha256-/8fggERlHySyimrGOHkDERbCPZJWqojycaifNPF6MjE=";
--- a/pkgs/development/tools/language-servers/helm-ls/default.nix
+++ b/pkgs/development/tools/language-servers/helm-ls/default.nix
@ -8,16 +8,16 @@

 buildGoModule rec {
  pname = "helm-ls";
-  version = "0.0.10";
+  version = "0.0.14";

  src = fetchFromGitHub {
    owner = "mrjosh";
    repo = "helm-ls";
    rev = "v${version}";
-    hash = "sha256-m+kr1NIrWqQGbWxOOu2mbPEk3AQPt8KqsByylUanbTM=";
+    hash = "sha256-h6s4mQgahFkGHiFcSS+HjUKzOT4x82UQMR19JWX09n0=";
  };

-  vendorHash = "sha256-8mSX7fwgxwZ8aIXfv3WxLiVH5PjSFzcxM0oekod84tA=";
+  vendorHash = "sha256-pV1FYhBLP0goetSr9v9iqXbeFTUHLdiIQ3ixqOsmp+Q=";

  nativeBuildInputs = [ installShellFiles ];

--- a/pkgs/development/tools/misc/lttng-tools/default.nix
+++ b/pkgs/development/tools/misc/lttng-tools/default.nix
@ -2,11 +2,11 @@

 stdenv.mkDerivation rec {
  pname = "lttng-tools";
-  version = "2.13.11";
+  version = "2.13.12";

  src = fetchurl {
    url = "https://lttng.org/files/lttng-tools/${pname}-${version}.tar.bz2";
-    sha256 = "sha256-rFuu75+mkJNrHKAezRdC2nYsLAhRH/G06SOTjZTQ+Xk=";
+    sha256 = "sha256-4S/lZjyvKtOne2BThRc9Tik33SFm2uecdPBkS/I5mK0=";
  };

  nativeBuildInputs = [ pkg-config ];
--- a/pkgs/development/tools/zed/default.nix
+++ b/pkgs/development/tools/zed/default.nix
@ -7,13 +7,13 @@

 buildGoModule rec {
  pname = "zed";
-  version = "1.14.0";
+  version = "1.15.0";

  src = fetchFromGitHub {
    owner = "brimdata";
    repo = pname;
    rev = "v${version}";
-    sha256 = "sha256-1k5qw/uWe5gtDUjDcMW54ezoXOBLt4T9lRmiOS06hz8=";
+    sha256 = "sha256-XY8vLCflNgxM75cTaUaqJPg8ZIm5dealC6K8es/5F5Q=";
  };

  vendorHash = "sha256-X1rE6/sgpB6jeTjLZJL/a7ghjRJYTXSQDHB4PmEFUmU=";
--- a/pkgs/games/prismlauncher/wrapper.nix
+++ b/pkgs/games/prismlauncher/wrapper.nix
@ -18,6 +18,7 @@
 , openal
 , jdk8
 , jdk17
+, jdk21
 , gamemode
 , flite
 , mesa-demos
@ -39,7 +40,7 @@
  # itself can take slightly longer to start
 , withWaylandGLFW ? false

-, jdks ? [ jdk17 jdk8 ]
+, jdks ? [ jdk21 jdk17 jdk8 ]
 , additionalLibs ? [ ]
 , additionalPrograms ? [ ]
 }:
--- a/pkgs/os-specific/linux/firmware/sof-firmware/default.nix
+++ b/pkgs/os-specific/linux/firmware/sof-firmware/default.nix
@ -5,11 +5,11 @@

 stdenvNoCC.mkDerivation rec {
  pname = "sof-firmware";
-  version = "2023.12.1";
+  version = "2024.03";

  src = fetchurl {
    url = "https://github.com/thesofproject/sof-bin/releases/download/v${version}/sof-bin-${version}.tar.gz";
-    sha256 = "sha256-6ied38mcWxHWNPH10jN/bVwNw4HOMxR5D3tVDkCI5nQ=";
+    sha256 = "sha256-T9ky97vBUXsG+nkR5tVmgU1dxP7FYIvbROfE/kkp+/Y=";
  };

  dontFixup = true; # binaries must not be stripped or patchelfed
--- a/pkgs/os-specific/linux/libbpf/default.nix
+++ b/pkgs/os-specific/linux/libbpf/default.nix
@ -47,7 +47,7 @@ stdenv.mkDerivation rec {
  # outputs = [ "out" "dev" ];

  meta = with lib; {
-    description = "Upstream mirror of libbpf";
+    description = "Library for loading eBPF programs and reading and manipulating eBPF objects from user-space";
    homepage = "https://github.com/libbpf/libbpf";
    license = with licenses; [ lgpl21 /* or */ bsd2 ];
    maintainers = with maintainers; [ thoughtpolice vcunat saschagrunert martinetd ];
--- a/pkgs/servers/etcd/3.5/default.nix
+++ b/pkgs/servers/etcd/3.5/default.nix
@ -1,11 +1,11 @@
 { lib, buildGoModule, fetchFromGitHub, symlinkJoin, nixosTests, k3s }:

 let
-  version = "3.5.12";
-  etcdSrcHash = "sha256-Z2WXNzFJYfRQCldUspQjUR5NyUzCCINycuEXWaTn4vU=";
-  etcdServerVendorHash = "sha256-S5cEIV4hKRjn9JFEKWBiSEPytHtVacsSnG6T8dofgyk=";
-  etcdUtlVendorHash = "sha256-Vgp44Kg6zUDYVJU6SiYd8ZEcAWqKPPTsqYafcfk89Cc=";
-  etcdCtlVendorHash = "sha256-PZLsekZzwlGzccCirNk9uUj70Ue5LMDs6LMWBI9yivs=";
+  version = "3.5.13";
+  etcdSrcHash = "sha256-6dQXgM6VEWwv5CfHvxxPxdhMwNjFsinwhsbSqvQoDxI=";
+  etcdServerVendorHash = "sha256-PB4gACfeYhdOXYs0xbcq2CmSMJnf/ifX2U2DN6zfJ1o=";
+  etcdUtlVendorHash = "sha256-f23mn4zE6beM8yPSbs9gEEEifyF2D+CVKdlYwQtzAkQ=";
+  etcdCtlVendorHash = "sha256-gSlyhmLKarDwc+MhYuTeTqwj0wLiN6+k2bHEVVTkyPc=";

  src = fetchFromGitHub {
    owner = "etcd-io";
--- a/pkgs/servers/http/apache-httpd/2.4.nix
+++ b/pkgs/servers/http/apache-httpd/2.4.nix
@ -1,5 +1,4 @@
 { lib, stdenv, fetchurl, perl, zlib, apr, aprutil, pcre2, libiconv, lynx, which, libxcrypt
-, fetchpatch
 , nixosTests
 , proxySupport ? true
 , sslSupport ? true, openssl
@ -13,11 +12,11 @@

 stdenv.mkDerivation rec {
  pname = "apache-httpd";
-  version = "2.4.58";
+  version = "2.4.59";

  src = fetchurl {
    url = "mirror://apache/httpd/httpd-${version}.tar.bz2";
-    sha256 = "sha256-+hbXKgeCEKVMR91b7y+Lm4oB2UkJpRRTlWs+xkQupMU=";
+    hash = "sha256-7FFQHsSAKE/1L2NyWBNdMzIwp9Ipw6+m9sL5BA4yEyM=";
  };

  # FIXME: -dev depends on -doc
@ -36,20 +35,6 @@ stdenv.mkDerivation rec {
    lib.optional http2Support nghttp2 ++
    lib.optional stdenv.isDarwin libiconv;

-  patches = lib.optionals modTlsSupport [
-    (fetchpatch {
-      name = "compat-with-rustls-ffi-0.10.0.patch";
-      url = "https://github.com/apache/httpd/commit/918620a183d843fb393ed939423a25d42c1044ec.patch";
-      hash = "sha256-YZi3t++hjM0skisax2xuh9DifZVZjCjVn6XQr6QKGEs=";
-    })
-  ] ++ lib.optionals libxml2Support [
-    (fetchpatch {
-      name = "compat-with-libxml2-2.12.patch";
-      url = "https://github.com/apache/httpd/commit/27a68e54b7c6d2ae80dca396fd2727852897dab1.patch";
-      hash = "sha256-k2EqCaDkckrXLsHnjP4h+b1brTnde4pUyrbOiPFB6qk=";
-    })
-  ];
-
  postPatch = ''
    sed -i config.layout -e "s|installbuilddir:.*|installbuilddir: $dev/share/build|"
    sed -i support/apachectl.in -e 's|@LYNX_PATH@|${lynx}/bin/lynx|'
--- a/pkgs/servers/peertube/default.nix
+++ b/pkgs/servers/peertube/default.nix
@ -45,13 +45,13 @@ let
 in
 stdenv.mkDerivation rec {
  pname = "peertube";
-  version = "6.0.3";
+  version = "6.0.4";

  src = fetchFromGitHub {
    owner = "Chocobozzz";
    repo = "PeerTube";
    rev = "v${version}";
-    hash = "sha256-Pskxfi+qqVk75hu22niLNFsToCJks1k8w8mTnXjr6jg=";
+    hash = "sha256-FxXIvibwdRcv8OaTQEXiM6CvWOIptfQXDQ1/PW910wg=";
  };

  yarnOfflineCacheServer = fetchYarnDeps {
--- a/pkgs/servers/prowlarr/default.nix
+++ b/pkgs/servers/prowlarr/default.nix
@ -21,15 +21,15 @@ let
  }.${stdenv.hostPlatform.system} or unsupported;

  hash = {
-    aarch64-darwin = "sha256-mHXoX526X0PYNViHgAdCPTRX6cqzlCyYLybdY1LRS8c=";
-    aarch64-linux = "sha256-wgHASkz6RMtKzBehnbqXsNbF057eK0i6xpOmuefMVx8=";
-    x86_64-darwin = "sha256-3EkGKDDsuUdbTvBILBClwPVvXN5JzTWGHBaG2lmHQ7s=";
-    x86_64-linux = "sha256-l24/thKqDCJQbeirSYiL5sqH8LRs7k3rk0qY6DZQvD8=";
+    aarch64-darwin = "sha256-ImivrfKromlA4753KUJIJCZr3yFYm/fWEqK6veEJBfw=";
+    aarch64-linux = "sha256-6UvjzheFkIRE1m0Wglhuch8oL5mmZoVMd9mtS7Gz7JQ=";
+    x86_64-darwin = "sha256-SvdMYwTcSm+Ozs2eBgTtjgMcUpgHK+VfQqmhPwD7VIk=";
+    x86_64-linux = "sha256-9yGQ7f28hTo+WKr6wqrSqMUqMTeRuq1cBs9e2INQfqM=";
  }.${stdenv.hostPlatform.system} or unsupported;

 in stdenv.mkDerivation rec {
  inherit pname;
-  version = "1.14.3.4333";
+  version = "1.15.0.4361";

  src = fetchurl {
    url = "https://github.com/Prowlarr/Prowlarr/releases/download/v${version}/Prowlarr.master.${version}.${os}-core-${arch}.tar.gz";
--- a/pkgs/servers/readarr/default.nix
+++ b/pkgs/servers/readarr/default.nix
@ -8,13 +8,13 @@ let
    x86_64-darwin = "x64";
  }."${stdenv.hostPlatform.system}" or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
  hash = {
-    x64-linux_hash = "sha256-4kCDbmq47wb7OuE5JzHPZ/mM9w6wcupFblJieu5dFxc=";
-    arm64-linux_hash = "sha256-Val9dEB4E3dnfeXT2ERwE+VoITSXeA7Lc51dyz1jJyQ=";
-    x64-osx_hash = "sha256-LvjAeftlNw5F6YFyhKLW9Fv9UIk6AgnGnxOu6ctmQNg=";
+    x64-linux_hash = "sha256-dPiavOh69pFWgzM533P7Cv0IUa3YOmCBROjdXflya0s=";
+    arm64-linux_hash = "sha256-dzGdOm4Uj1RavpwLQ5PmeeCBELoTZz7VCtuv9+cZPxQ=";
+    x64-osx_hash = "sha256-i5KKY1r2zlIRPggoo9Ju7WSkHA44x42thVQswnXYAp4=";
  }."${arch}-${os}_hash";
 in stdenv.mkDerivation rec {
  pname = "readarr";
-  version = "0.3.20.2452";
+  version = "0.3.21.2475";

  src = fetchurl {
    url = "https://github.com/Readarr/Readarr/releases/download/v${version}/Readarr.develop.${version}.${os}-core-${arch}.tar.gz";
--- a/pkgs/servers/samba/4.x.nix
+++ b/pkgs/servers/samba/4.x.nix
@ -61,11 +61,11 @@ let
 in
 stdenv.mkDerivation rec {
  pname = "samba";
-  version = "4.19.5";
+  version = "4.20.0";

  src = fetchurl {
    url = "mirror://samba/pub/samba/stable/${pname}-${version}.tar.gz";
-    hash = "sha256-DiQFtM7CnQRZYh9DQKGnSvdx7Hz/7f9DJQytfx+HYF4=";
+    hash = "sha256-AmclQlEKxuXQyRwMFNkKtObsOXxwnpUsbaOm4LTVpC8=";
  };

  outputs = [ "out" "dev" "man" ];
--- a/pkgs/servers/search/groonga/default.nix
+++ b/pkgs/servers/search/groonga/default.nix
@ -6,11 +6,11 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "groonga";
-  version = "14.0.1";
+  version = "14.0.2";

  src = fetchurl {
    url = "https://packages.groonga.org/source/groonga/groonga-${finalAttrs.version}.tar.gz";
-    hash = "sha256-zXiDXYSvdyQ2HBZHUZaYHtZMs7BjzHJaix1ShLbkWtA=";
+    hash = "sha256-o9C6lPOPkb2KCbF4CqLyKtXHfOdB3jAIv5P6SjTJAJc=";
  };

  patches = [
--- a/pkgs/shells/fish/plugins/wakatime-fish.nix
+++ b/pkgs/shells/fish/plugins/wakatime-fish.nix
@ -6,13 +6,13 @@

 buildFishPlugin rec {
  pname = "wakatime-fish";
-  version = "0.0.5";
+  version = "0.0.6";

  src = fetchFromGitHub {
    owner = "ik11235";
    repo = "wakatime.fish";
    rev = "v${version}";
-    hash = "sha256-BYDff4OP4Sg5I7p0GviZKSDulx468ePZigigyTdtkqM=";
+    hash = "sha256-Hsr69n4fCvPc64NztgaBZQuR0znkzlL8Uotw9Jf2S1o=";
  };

  preFixup = ''
--- a/pkgs/tools/admin/syft/default.nix
+++ b/pkgs/tools/admin/syft/default.nix
@ -1,14 +1,19 @@
-{ lib, buildGoModule, fetchFromGitHub, installShellFiles }:
+{
+  lib,
+  buildGoModule,
+  fetchFromGitHub,
+  installShellFiles,
+}:

 buildGoModule rec {
  pname = "syft";
-  version = "1.1.0";
+  version = "1.1.1";

  src = fetchFromGitHub {
    owner = "anchore";
-    repo = pname;
-    rev = "v${version}";
-    hash = "sha256-VLCxbD9LFXH8bdc2v9RB/vlLZtg1ekDotZi1xwORdjc=";
+    repo = "syft";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-75puiKfXp8vS9iiSk6R85RBn9xlQp9jk51ZNBeJXc/U=";
    # populate values that require us to use git. By doing this in postFetch we
    # can delete .git afterwards and maintain better reproducibility of the src.
    leaveDotGit = true;
@ -22,7 +27,8 @@ buildGoModule rec {
  };
  # hash mismatch with darwin
  proxyVendor = true;
-  vendorHash = "sha256-eJCXRXeYAk3VTe+RcFjjKUbKCniPKY1wPXsBpZjeCNw=";
+
+  vendorHash = "sha256-AHzKmitIUw0CqBU2Xinb6UVnlZB+2ED85uqGUFonkWM=";

  nativeBuildInputs = [ installShellFiles ];

@ -31,9 +37,9 @@ buildGoModule rec {
  ldflags = [
    "-s"
    "-w"
-    "-X main.version=${version}"
-    "-X main.gitDescription=v${version}"
-    "-X main.gitTreeState=clean"
+    "-X=main.version=${version}"
+    "-X=main.gitDescription=v${version}"
+    "-X=main.gitTreeState=clean"
  ];

  preBuild = ''
@ -66,16 +72,20 @@ buildGoModule rec {
  '';

  meta = with lib; {
+    description = "CLI tool and library for generating a Software Bill of Materials from container images and filesystems";
    homepage = "https://github.com/anchore/syft";
    changelog = "https://github.com/anchore/syft/releases/tag/v${version}";
-    description = "CLI tool and library for generating a Software Bill of Materials from container images and filesystems";
    longDescription = ''
      A CLI tool and Go library for generating a Software Bill of Materials
      (SBOM) from container images and filesystems. Exceptional for
      vulnerability detection when used with a scanner tool like Grype.
    '';
    license = with licenses; [ asl20 ];
-    maintainers = with maintainers; [ jk developer-guy kashw2 ];
+    maintainers = with maintainers; [
+      developer-guy
+      jk
+      kashw2
+    ];
    mainProgram = "syft";
  };
 }
--- a/pkgs/tools/bootloaders/refind/default.nix
+++ b/pkgs/tools/bootloaders/refind/default.nix
@ -5,6 +5,7 @@
 , nixosTests
 , efibootmgr
 , openssl
+, withSbsigntool ? false # currently, cross compiling sbsigntool is broken, so default to false
 , sbsigntool
 , makeWrapper
 }:
@ -112,7 +113,7 @@ stdenv.mkDerivation rec {

  postInstall = ''
    wrapProgram $out/bin/refind-install \
-      --prefix PATH : ${lib.makeBinPath [ efibootmgr openssl sbsigntool ]}
+      --prefix PATH : ${lib.makeBinPath ( [ efibootmgr openssl ] ++ lib.optional withSbsigntool sbsigntool )}
    wrapProgram $out/bin/refind-mvrefind \
      --prefix PATH : ${lib.makeBinPath [ efibootmgr ]}
  '';
--- a/pkgs/tools/filesystems/mtdutils/default.nix
+++ b/pkgs/tools/filesystems/mtdutils/default.nix
@ -2,12 +2,12 @@

 stdenv.mkDerivation rec {
  pname = "mtd-utils";
-  version = "2.1.6";
+  version = "2.2.0";

  src = fetchgit {
    url = "git://git.infradead.org/mtd-utils.git";
    rev = "v${version}";
-    sha256 = "sha256-NMYzUPt/91lv8f7E1ytX91SqwbBEOtHjCL54EcumcZA=";
+    sha256 = "sha256-uYXzZnVL5PkyDAntH8YsocwmQ8tf1f0Vl78SdE2B+Oc=";
  };

  nativeBuildInputs = [ autoreconfHook pkg-config ] ++ lib.optional doCheck cmocka;
--- a/pkgs/tools/misc/cyberchef/default.nix
+++ b/pkgs/tools/misc/cyberchef/default.nix
@ -5,11 +5,11 @@

 stdenv.mkDerivation rec {
  pname = "cyberchef";
-  version = "10.9.0";
+  version = "10.15.0";

  src = fetchzip {
    url = "https://github.com/gchq/CyberChef/releases/download/v${version}/CyberChef_v${version}.zip";
-    sha256 = "sha256-lsQC86gTfDQy7wonoYdQitdF+4hn8qyFpXKg+AL5TnU=";
+    sha256 = "sha256-QXVqFMG6NJeeTON7w+46MjWXs1bIRL2ji047IvHgvYI=";
    stripRoot = false;
  };

--- a/pkgs/tools/misc/fastfetch/default.nix
+++ b/pkgs/tools/misc/fastfetch/default.nix
@ -8,6 +8,7 @@
 , dconf
 , ddcutil
 , glib
+, hwdata
 , imagemagick_light
 , libXrandr
 , libglvnd
@ -20,7 +21,6 @@
 , nix-update-script
 , ocl-icd
 , opencl-headers
-, pciutils
 , pcre
 , pcre2
 , pkg-config
@ -43,13 +43,13 @@

 stdenv.mkDerivation (finalAttrs: {
  pname = "fastfetch";
-  version = "2.8.10";
+  version = "2.9.0";

  src = fetchFromGitHub {
    owner = "fastfetch-cli";
    repo = "fastfetch";
    rev = finalAttrs.version;
-    hash = "sha256-MIrjfd1KudtU+4X65M+qdPtWUPWQXBlE13Myp1u8hPM=";
+    hash = "sha256-D9WErPf9Um7McUK465c2FzZkWz/+dtPSIFMA04ak7Y4=";
  };

  outputs = [ "out" "man" ];
@ -73,13 +73,13 @@ stdenv.mkDerivation (finalAttrs: {
    dconf
    ddcutil
    glib
+    hwdata
    libpulseaudio
    libselinux
    libsepol
    networkmanager
    ocl-icd
    opencl-headers
-    pciutils
    util-linux
    zlib
  ] ++ lib.optionals rpmSupport [
--- a/pkgs/tools/misc/rmlint/default.nix
+++ b/pkgs/tools/misc/rmlint/default.nix
@ -1,11 +1,11 @@
 { lib, stdenv
 , cairo
+, elfutils
 , fetchFromGitHub
 , glib
 , gobject-introspection
 , gtksourceview3
 , json-glib
-, libelf
 , makeWrapper
 , pango
 , pkg-config
@ -48,7 +48,6 @@ stdenv.mkDerivation rec {
  buildInputs = [
    glib
    json-glib
-    libelf
    util-linux
  ] ++ lib.optionals withGui [
    cairo
@ -57,6 +56,8 @@ stdenv.mkDerivation rec {
    polkit
    python3
    python3.pkgs.pygobject3
+  ] ++ lib.optionals (lib.meta.availableOn stdenv.hostPlatform elfutils) [
+    elfutils
  ];

  prePatch = ''
--- a/pkgs/tools/security/pinentry/default.nix
+++ b/pkgs/tools/security/pinentry/default.nix
@ -103,7 +103,7 @@ let
          platforms.all;
        longDescription = ''
          Pinentry provides a console and (optional) GTK and Qt GUIs allowing users
-          to enter a passphrase when `gpg' or `gpg2' is run and needs it.
+          to enter a passphrase when `gpg` or `gpg2` is run and needs it.
        '';
        maintainers = with maintainers; [ fpletz ];
        mainProgram = "pinentry";
--- a/pkgs/tools/security/vals/default.nix
+++ b/pkgs/tools/security/vals/default.nix
@ -2,16 +2,16 @@

 buildGoModule rec {
  pname = "vals";
-  version = "0.36.0";
+  version = "0.37.0";

  src = fetchFromGitHub {
    rev = "v${version}";
    owner = "helmfile";
    repo = pname;
-    sha256 = "sha256-jD7fYvPOR6fwpCqNhxNXzjc8qtmjXkJy+f/L7t9Jlu4=";
+    sha256 = "sha256-R/nTlB8VM41Yah+3sH/J3Y3m9KUFsIZQNQ9kFddo+Mo=";
  };

-  vendorHash = "sha256-b4GmDzRvWQzoKzQo7am/3M9cFqO+QNW4UxlWZrPswiA=";
+  vendorHash = "sha256-VKJIbsVIIEEGqo+LXfYzhIJLtcj0jbbq/UXVpykgcz8=";

  ldflags = [
    "-s"
--- a/pkgs/tools/system/thermald/default.nix
+++ b/pkgs/tools/system/thermald/default.nix
@ -10,7 +10,6 @@
 , libevdev
 , libtool
 , libxml2
-, xz
 , pkg-config
 , lib, stdenv
 , upower
@ -18,7 +17,7 @@

 stdenv.mkDerivation rec {
  pname = "thermald";
-  version = "2.5.6";
+  version = "2.5.7";

  outputs = [ "out" "devdoc" ];

@ -26,7 +25,7 @@ stdenv.mkDerivation rec {
    owner = "intel";
    repo = "thermal_daemon";
    rev = "v${version}";
-    sha256 = "sha256-7QoHq3NtBtGJ/ihiAkGWBng9mP+NAUiNX03Fb4T11cg=";
+    sha256 = "sha256-FU9nPuyCWMEmx2i3YTT/Y3BYinYU0MBCOjH5Pm3LENA=";
  };

  nativeBuildInputs = [
@ -45,7 +44,6 @@ stdenv.mkDerivation rec {
    dbus-glib
    libevdev
    libxml2
-    xz
    upower
  ];

--- a/pkgs/tools/text/fanficfare/default.nix
+++ b/pkgs/tools/text/fanficfare/default.nix
@ -2,12 +2,12 @@

 python3Packages.buildPythonApplication rec {
  pname = "FanFicFare";
-  version = "4.32.3";
+  version = "4.33.0";
  pyproject = true;

  src = fetchPypi {
    inherit pname version;
-    hash = "sha256-Qfe24Ees3LLnSuU4kjn+dwtKjLBSYgF22U1YAtpw1po=";
+    hash = "sha256-1s3YeI4deej+lkDXtFzfBOtATY+jx+KB7JAnLUDZK8w=";
  };

  nativeBuildInputs = with python3Packages; [
--- a/pkgs/tools/virtualization/govc/default.nix
+++ b/pkgs/tools/virtualization/govc/default.nix
@ -2,7 +2,7 @@

 buildGoModule rec {
  pname = "govc";
-  version = "0.36.2";
+  version = "0.36.3";

  subPackages = [ "govc" ];

@ -10,7 +10,7 @@ buildGoModule rec {
    rev = "v${version}";
    owner = "vmware";
    repo = "govmomi";
-    sha256 = "sha256-1Ap15DE+Fe76mDxrfeiVTYhur5GjZj0FzjvKDDWbhsg=";
+    sha256 = "sha256-R/YqP7vrgfTeRVf6VDFdY2GGtHJZmZm1z/QA9tIE9HE=";
  };

  vendorHash = "sha256-1EAQMYaTEtfAiu7+UTkC7QZwSWC1Ihwj9leTd90T0ZU=";
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@ -1830,6 +1830,12 @@ with pkgs;

  github-copilot-cli = callPackage ../tools/misc/github-copilot-cli { };

+  # This is to workaround gfal2-python broken against Python 3.12 or later.
+  # TODO: Remove these lines after solving the breakage.
+  gfal2-util = callPackage ../by-name/gf/gfal2-util/package.nix (lib.optionalAttrs python3Packages.gfal2-python.meta.broken {
+    python3Packages = python311Packages;
+  });
+
  gfshare = callPackage ../tools/security/gfshare { };

  gh-actions-cache = callPackage ../tools/misc/gh-actions-cache { };
@ -2962,8 +2968,6 @@ with pkgs;

  spaceFM = callPackage ../applications/file-managers/spacefm { };

-  tuifimanager = callPackage ../applications/file-managers/tuifimanager { };
-
  vifm = callPackage ../applications/file-managers/vifm { };

  vifm-full = vifm.override {
@ -31714,8 +31718,6 @@ with pkgs;
    withDoc = true;
  };

-  gpscorrelate = callPackage ../applications/misc/gpscorrelate { };
-
  gpsd = callPackage ../servers/gpsd { };

  gpsprune = callPackage ../applications/misc/gpsprune { };
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@ -4702,6 +4702,12 @@ self: super: with self; {

  gevent-websocket = callPackage ../development/python-modules/gevent-websocket { };

+  gfal2-python = callPackage ../development/python-modules/gfal2-python { };
+
+  gfal2-util = callPackage ../development/python-modules/gfal2-util {
+    inherit (pkgs) xrootd;
+  };
+
  gflags = callPackage ../development/python-modules/gflags { };

  gflanguages = callPackage ../development/python-modules/gflanguages { };