From 831dbf4e0a8ce8d1b4d2830ead35461aba4a72ac Mon Sep 17 00:00:00 2001
From: kfollesdal <kristoffer.follesdal@bkk.no>
Date: Mon, 8 Mar 2021 09:36:02 +0100
Subject: [PATCH 01/32] nixos/virtualisation/azure-common: add auto resize of
 os disk

At the moment os disk do not automatically expand in Azure. This commit
fixes this so os disk expands to whole disk when created or changed.
---
 nixos/modules/virtualisation/azure-common.nix | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/nixos/modules/virtualisation/azure-common.nix b/nixos/modules/virtualisation/azure-common.nix
index 8efa177e30d..dc7853b9503 100644
--- a/nixos/modules/virtualisation/azure-common.nix
+++ b/nixos/modules/virtualisation/azure-common.nix
@@ -21,7 +21,11 @@ with lib;
   # way to select them anyway.
   boot.loader.grub.configurationLimit = 0;
 
-  fileSystems."/".device = "/dev/disk/by-label/nixos";
+  fileSystems."/" = {
+    device = "/dev/disk/by-label/nixos";
+    fsType = "ext4";
+    autoResize = true;
+  };
 
   # Allow root logins only using the SSH key that the user specified
   # at instance creation time, ping client connections to avoid timeouts

From 03d38f77498c155c5439dbf596409a7f9ff2c0e0 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Tue, 1 Mar 2022 01:27:51 +0000
Subject: [PATCH 02/32] azure-storage-azcopy: 10.13.0 -> 10.14.0

---
 pkgs/development/tools/azcopy/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/tools/azcopy/default.nix b/pkgs/development/tools/azcopy/default.nix
index 27d1c866725..4e85770a7f2 100644
--- a/pkgs/development/tools/azcopy/default.nix
+++ b/pkgs/development/tools/azcopy/default.nix
@@ -2,18 +2,18 @@
 
 buildGoModule rec {
   pname = "azure-storage-azcopy";
-  version = "10.13.0";
+  version = "10.14.0";
 
   src = fetchFromGitHub {
     owner = "Azure";
     repo = "azure-storage-azcopy";
     rev = "v${version}";
-    sha256 = "sha256-L5gfS2hwk1uaWEygn+liupdANL9qizHAjxNz25KBwaY=";
+    sha256 = "sha256-9NuX4BbQx/ZeWvyTxlZjrb7ETwSFwBpfDcSt8qvKAxE=";
   };
 
   subPackages = [ "." ];
 
-  vendorSha256 = "sha256-ePEpc18Y99Moe/aj8n1+no6D70vZoIEjC023Uup98Uo=";
+  vendorSha256 = "sha256-9ThsJySzsyS0eX/0BlAAvtaeJpPYCP0cN1YgIShYrKw=";
 
   doCheck = false;
 

From 6fb7d8e67593549838da839f7435156f1fd81f31 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 4 Mar 2022 19:38:22 +0000
Subject: [PATCH 03/32] tmux-mem-cpu-load: 3.5.1 -> 3.6.0

---
 pkgs/tools/misc/tmux-mem-cpu-load/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/misc/tmux-mem-cpu-load/default.nix b/pkgs/tools/misc/tmux-mem-cpu-load/default.nix
index 45a5edd6ae5..7370a21512d 100644
--- a/pkgs/tools/misc/tmux-mem-cpu-load/default.nix
+++ b/pkgs/tools/misc/tmux-mem-cpu-load/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "tmux-mem-cpu-load";
-  version = "3.5.1";
+  version = "3.6.0";
 
   src = fetchFromGitHub {
     owner = "thewtex";
     repo = "tmux-mem-cpu-load";
     rev = "v${version}";
-    sha256 = "sha256-4ZMF+RacZL9dJRCz63XPNuigTKHOW+ZcA4vB4jsnASc=";
+    sha256 = "sha256-1smhlp30y0qihm+d9RcCKY1CFbPm5gzago+OIQQT5jE=";
   };
 
   nativeBuildInputs = [ cmake ];

From a9aa5ccb3a01ee8d04c5e8f5b9693c8b2539d38c Mon Sep 17 00:00:00 2001
From: oxalica <oxalicc@pm.me>
Date: Wed, 16 Mar 2022 15:48:50 +0800
Subject: [PATCH 04/32] taskwarrior: 2.6.1 -> 2.6.2

---
 pkgs/applications/misc/taskwarrior/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/misc/taskwarrior/default.nix b/pkgs/applications/misc/taskwarrior/default.nix
index 8290a868ef0..5a12380a4ff 100644
--- a/pkgs/applications/misc/taskwarrior/default.nix
+++ b/pkgs/applications/misc/taskwarrior/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "taskwarrior";
-  version = "2.6.1";
+  version = "2.6.2";
 
   src = fetchFromGitHub {
     owner = "GothenburgBitFactory";
     repo = "taskwarrior";
     rev = "v${version}";
-    sha256 = "sha256-jMZzo2cegoapEHTvfD6ThU1IsXru3iOcpyDbZxkSXzQ=";
+    sha256 = "sha256-0YveqiylXJi4cdDCfnPtwCVOJbQrZYsxnXES+9B4Yfw=";
     fetchSubmodules = true;
   };
 

From 729988f5c66734bab710b691b778929eb86a4b1e Mon Sep 17 00:00:00 2001
From: Abraham Chan <abraham@rangeme.com>
Date: Wed, 16 Mar 2022 23:00:28 +1100
Subject: [PATCH 05/32] elasticsearch7: add darwin-aarch64

---
 pkgs/servers/search/elasticsearch/7.x.nix | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/pkgs/servers/search/elasticsearch/7.x.nix b/pkgs/servers/search/elasticsearch/7.x.nix
index 592cc947a42..83c169eb25e 100644
--- a/pkgs/servers/search/elasticsearch/7.x.nix
+++ b/pkgs/servers/search/elasticsearch/7.x.nix
@@ -18,9 +18,10 @@ let
   plat = elemAt info 1;
   shas =
     {
-      x86_64-linux  = "1s16l95wc589cr69pfbgmkn9rkvxn6sd6jlbiqpm6p6iyxiaxd6c";
-      x86_64-darwin = "05h7pvq4pb816wgcymnfklp3w6sv54x6138v2infw5219dnk8pfs";
-      aarch64-linux = "0q4xnjzhlx1b2lkikca88qh9glfxaifsm419k2bxxlrfrx31zlkq";
+      x86_64-linux   = "1s16l95wc589cr69pfbgmkn9rkvxn6sd6jlbiqpm6p6iyxiaxd6c";
+      x86_64-darwin  = "05h7pvq4pb816wgcymnfklp3w6sv54x6138v2infw5219dnk8pfs";
+      aarch64-linux  = "0q4xnjzhlx1b2lkikca88qh9glfxaifsm419k2bxxlrfrx31zlkq";
+      aarch64-darwin = "067mb1dianwiarw8cz1va4g6zfhp9ls4s174xbpkxwsknvvyhgz6";
     };
 in
 stdenv.mkDerivation rec {
@@ -44,7 +45,8 @@ stdenv.mkDerivation rec {
       "ES_CLASSPATH=\"\$ES_CLASSPATH:$out/\$additional_classpath_directory/*\""
   '';
 
-  nativeBuildInputs = [ autoPatchelfHook makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ]
+    ++ lib.optional (!stdenv.hostPlatform.isDarwin) autoPatchelfHook;
 
   buildInputs = [ jre_headless util-linux zlib ];
 

From d2efc3ef70401636ca117b9a4025c0ce2121f0a0 Mon Sep 17 00:00:00 2001
From: Jan Tojnar <jtojnar@gmail.com>
Date: Thu, 17 Mar 2022 04:04:10 +0100
Subject: [PATCH 06/32] nixos/networkmanager: Allow overriding installed
 plug-ins

Now, one can just use `networking.networkmanager.plugins = lib.mkForce [];`
if they want to get rid of the plug-ins.

Co-authored-by: lassulus <lassulus@lassul.us>
---
 .../services/networking/networkmanager.nix    | 106 +++++++++---------
 .../networkmanager/fortisslvpn/default.nix    |   1 +
 .../networkmanager/iodine/default.nix         |   1 +
 .../networkmanager/l2tp/default.nix           |   4 +
 .../networkmanager/openconnect/default.nix    |   1 +
 .../networkmanager/openvpn/default.nix        |   1 +
 .../networkmanager/sstp/default.nix           |   1 +
 .../networkmanager/strongswan/default.nix     |   4 +
 .../networkmanager/vpnc/default.nix           |   1 +
 9 files changed, 69 insertions(+), 51 deletions(-)

diff --git a/nixos/modules/services/networking/networkmanager.nix b/nixos/modules/services/networking/networkmanager.nix
index 7a9d9e5428a..2b3577eb92c 100644
--- a/nixos/modules/services/networking/networkmanager.nix
+++ b/nixos/modules/services/networking/networkmanager.nix
@@ -5,18 +5,6 @@ with lib;
 let
   cfg = config.networking.networkmanager;
 
-  basePackages = with pkgs; [
-    modemmanager
-    networkmanager
-    networkmanager-fortisslvpn
-    networkmanager-iodine
-    networkmanager-l2tp
-    networkmanager-openconnect
-    networkmanager-openvpn
-    networkmanager-vpnc
-    networkmanager-sstp
-   ] ++ optional (!delegateWireless && !enableIwd) wpa_supplicant;
-
   delegateWireless = config.networking.wireless.enable == true && cfg.unmanaged != [];
 
   enableIwd = cfg.wifi.backend == "iwd";
@@ -145,6 +133,15 @@ let
     '';
   };
 
+  packages = [
+    pkgs.modemmanager
+    pkgs.networkmanager
+  ]
+  ++ cfg.plugins
+  ++ lib.optionals (!delegateWireless && !enableIwd) [
+    pkgs.wpa_supplicant
+  ];
+
 in {
 
   meta = {
@@ -227,13 +224,29 @@ in {
         '';
       };
 
-      packages = mkOption {
-        type = types.listOf types.package;
+      plugins = mkOption {
+        type =
+          let
+            networkManagerPluginPackage = types.package // {
+              description = "NetworkManager plug-in";
+              check =
+                p:
+                lib.assertMsg
+                  (types.package.check p
+                    && p ? networkManagerPlugin
+                    && lib.isString p.networkManagerPlugin)
+                  ''
+                    Package ‘${p.name}’, is not a NetworkManager plug-in.
+                    Those need to have a ‘networkManagerPlugin’ attribute.
+                  '';
+            };
+          in
+          types.listOf networkManagerPluginPackage;
         default = [ ];
         description = ''
-          Extra packages that provide NetworkManager plugins.
+          List of NetworkManager plug-ins to enable.
+          Some plug-ins are enabled by the NetworkManager module by default.
         '';
-        apply = list: basePackages ++ list;
       };
 
       dhcp = mkOption {
@@ -380,7 +393,7 @@ in {
           </para><para>
           If you enable this option the
           <literal>networkmanager_strongswan</literal> plugin will be added to
-          the <option>networking.networkmanager.packages</option> option
+          the <option>networking.networkmanager.plugins</option> option
           so you don't need to to that yourself.
         '';
       };
@@ -399,6 +412,9 @@ in {
   };
 
   imports = [
+    (mkRenamedOptionModule
+      [ "networking" "networkmanager" "packages" ]
+      [ "networking" "networkmanager" "plugins" ])
     (mkRenamedOptionModule [ "networking" "networkmanager" "useDnsmasq" ] [ "networking" "networkmanager" "dns" ])
     (mkRemovedOptionModule ["networking" "networkmanager" "dynamicHosts"] ''
       This option was removed because allowing (multiple) regular users to
@@ -426,31 +442,12 @@ in {
 
     hardware.wirelessRegulatoryDatabase = true;
 
-    environment.etc = with pkgs; {
-      "NetworkManager/NetworkManager.conf".source = configFile;
-
-      "NetworkManager/VPN/nm-openvpn-service.name".source =
-        "${networkmanager-openvpn}/lib/NetworkManager/VPN/nm-openvpn-service.name";
-
-      "NetworkManager/VPN/nm-vpnc-service.name".source =
-        "${networkmanager-vpnc}/lib/NetworkManager/VPN/nm-vpnc-service.name";
-
-      "NetworkManager/VPN/nm-openconnect-service.name".source =
-        "${networkmanager-openconnect}/lib/NetworkManager/VPN/nm-openconnect-service.name";
-
-      "NetworkManager/VPN/nm-fortisslvpn-service.name".source =
-        "${networkmanager-fortisslvpn}/lib/NetworkManager/VPN/nm-fortisslvpn-service.name";
-
-      "NetworkManager/VPN/nm-l2tp-service.name".source =
-        "${networkmanager-l2tp}/lib/NetworkManager/VPN/nm-l2tp-service.name";
-
-      "NetworkManager/VPN/nm-iodine-service.name".source =
-        "${networkmanager-iodine}/lib/NetworkManager/VPN/nm-iodine-service.name";
-
-      "NetworkManager/VPN/nm-sstp-service.name".source =
-        "${networkmanager-sstp}/lib/NetworkManager/VPN/nm-sstp-service.name";
-
+    environment.etc = {
+        "NetworkManager/NetworkManager.conf".source = configFile;
       }
+      // builtins.listToAttrs (map (pkg: nameValuePair "NetworkManager/${pkg.networkManagerPlugin}" {
+        source = "${pkg}/lib/NetworkManager/${pkg.networkManagerPlugin}";
+      }) cfg.plugins)
       // optionalAttrs cfg.enableFccUnlock
          {
            "ModemManager/fcc-unlock.d".source =
@@ -460,18 +457,13 @@ in {
          {
            "NetworkManager/dispatcher.d/02overridedns".source = overrideNameserversScript;
          }
-      // optionalAttrs cfg.enableStrongSwan
-         {
-           "NetworkManager/VPN/nm-strongswan-service.name".source =
-             "${pkgs.networkmanager_strongswan}/lib/NetworkManager/VPN/nm-strongswan-service.name";
-         }
       // listToAttrs (lib.imap1 (i: s:
          {
             name = "NetworkManager/dispatcher.d/${dispatcherTypesSubdirMap.${s.type}}03userscript${lib.fixedWidthNumber 4 i}";
             value = { mode = "0544"; inherit (s) source; };
          }) cfg.dispatcherScripts);
 
-    environment.systemPackages = cfg.packages;
+    environment.systemPackages = packages;
 
     users.groups = {
       networkmanager.gid = config.ids.gids.networkmanager;
@@ -490,7 +482,7 @@ in {
       };
     };
 
-    systemd.packages = cfg.packages;
+    systemd.packages = packages;
 
     systemd.tmpfiles.rules = [
       "d /etc/NetworkManager/system-connections 0700 root root -"
@@ -534,8 +526,20 @@ in {
         useDHCP = false;
       })
 
+      {
+        networkmanager.plugins = with pkgs; [
+          networkmanager-fortisslvpn
+          networkmanager-iodine
+          networkmanager-l2tp
+          networkmanager-openconnect
+          networkmanager-openvpn
+          networkmanager-vpnc
+          networkmanager-sstp
+        ];
+      }
+
       (mkIf cfg.enableStrongSwan {
-        networkmanager.packages = [ pkgs.networkmanager_strongswan ];
+        networkmanager.plugins = [ pkgs.networkmanager_strongswan ];
       })
 
       (mkIf enableIwd {
@@ -559,10 +563,10 @@ in {
     security.polkit.enable = true;
     security.polkit.extraConfig = polkitConf;
 
-    services.dbus.packages = cfg.packages
+    services.dbus.packages = packages
       ++ optional cfg.enableStrongSwan pkgs.strongswanNM
       ++ optional (cfg.dns == "dnsmasq") pkgs.dnsmasq;
 
-    services.udev.packages = cfg.packages;
+    services.udev.packages = packages;
   };
 }
diff --git a/pkgs/tools/networking/networkmanager/fortisslvpn/default.nix b/pkgs/tools/networking/networkmanager/fortisslvpn/default.nix
index f97bac13cf7..da30fc6cbe1 100644
--- a/pkgs/tools/networking/networkmanager/fortisslvpn/default.nix
+++ b/pkgs/tools/networking/networkmanager/fortisslvpn/default.nix
@@ -74,6 +74,7 @@ stdenv.mkDerivation rec {
       attrPath = "networkmanager-fortisslvpn";
       versionPolicy = "odd-unstable";
     };
+    networkManagerPlugin = "VPN/nm-fortisslvpn-service.name";
   };
 
   meta = with lib; {
diff --git a/pkgs/tools/networking/networkmanager/iodine/default.nix b/pkgs/tools/networking/networkmanager/iodine/default.nix
index e56d9411b39..8c8d0dd6a32 100644
--- a/pkgs/tools/networking/networkmanager/iodine/default.nix
+++ b/pkgs/tools/networking/networkmanager/iodine/default.nix
@@ -48,6 +48,7 @@ in stdenv.mkDerivation {
       packageName = pname;
       attrPath = "networkmanager-iodine";
     };
+    networkManagerPlugin = "VPN/nm-iodine-service.name";
   };
 
   meta = with lib; {
diff --git a/pkgs/tools/networking/networkmanager/l2tp/default.nix b/pkgs/tools/networking/networkmanager/l2tp/default.nix
index 5f00c1fa9d8..88ccad59bd1 100644
--- a/pkgs/tools/networking/networkmanager/l2tp/default.nix
+++ b/pkgs/tools/networking/networkmanager/l2tp/default.nix
@@ -41,6 +41,10 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  passthru = {
+    networkManagerPlugin = "VPN/nm-l2tp-service.name";
+  };
+
   meta = with lib; {
     description = "L2TP plugin for NetworkManager";
     inherit (networkmanager.meta) platforms;
diff --git a/pkgs/tools/networking/networkmanager/openconnect/default.nix b/pkgs/tools/networking/networkmanager/openconnect/default.nix
index c03a698514a..fec313e820b 100644
--- a/pkgs/tools/networking/networkmanager/openconnect/default.nix
+++ b/pkgs/tools/networking/networkmanager/openconnect/default.nix
@@ -71,6 +71,7 @@ in stdenv.mkDerivation {
       attrPath = "networkmanager-openconnect";
       versionPolicy = "odd-unstable";
     };
+    networkManagerPlugin = "VPN/nm-openconnect-service.name";
   };
 
   meta = with lib; {
diff --git a/pkgs/tools/networking/networkmanager/openvpn/default.nix b/pkgs/tools/networking/networkmanager/openvpn/default.nix
index 20a90fffed2..d2cc69a5c5e 100644
--- a/pkgs/tools/networking/networkmanager/openvpn/default.nix
+++ b/pkgs/tools/networking/networkmanager/openvpn/default.nix
@@ -36,6 +36,7 @@ in stdenv.mkDerivation {
       attrPath = "networkmanager-openvpn";
       versionPolicy = "odd-unstable";
     };
+    networkManagerPlugin = "VPN/nm-openvpn-service.name";
   };
 
   meta = with lib; {
diff --git a/pkgs/tools/networking/networkmanager/sstp/default.nix b/pkgs/tools/networking/networkmanager/sstp/default.nix
index f4866234438..8b75db6495f 100644
--- a/pkgs/tools/networking/networkmanager/sstp/default.nix
+++ b/pkgs/tools/networking/networkmanager/sstp/default.nix
@@ -54,6 +54,7 @@ in stdenv.mkDerivation {
       packageName = pname;
       attrPath = "networkmanager-sstp";
     };
+    networkManagerPlugin = "VPN/nm-sstp-service.name";
   };
 
   meta = with lib; {
diff --git a/pkgs/tools/networking/networkmanager/strongswan/default.nix b/pkgs/tools/networking/networkmanager/strongswan/default.nix
index cebcec35a31..be0dcf234ff 100644
--- a/pkgs/tools/networking/networkmanager/strongswan/default.nix
+++ b/pkgs/tools/networking/networkmanager/strongswan/default.nix
@@ -24,6 +24,10 @@ stdenv.mkDerivation rec {
     "--with-nm-plugindir=$(out)/lib/NetworkManager"
   ];
 
+  passthru = {
+    networkManagerPlugin = "VPN/nm-strongswan-service.name";
+  };
+
   PKG_CONFIG_LIBNM_VPNSERVICEDIR = "$(out)/lib/NetworkManager/VPN";
 
   meta = with lib; {
diff --git a/pkgs/tools/networking/networkmanager/vpnc/default.nix b/pkgs/tools/networking/networkmanager/vpnc/default.nix
index 70e7104696e..a094e427188 100644
--- a/pkgs/tools/networking/networkmanager/vpnc/default.nix
+++ b/pkgs/tools/networking/networkmanager/vpnc/default.nix
@@ -40,6 +40,7 @@ in stdenv.mkDerivation {
       attrPath = "networkmanager-vpnc";
       versionPolicy = "odd-unstable";
     };
+    networkManagerPlugin = "VPN/nm-vpnc-service.name";
   };
 
   meta = with lib; {

From 6cfaf0a464edc98cf9f00258d20791905c5ebf2f Mon Sep 17 00:00:00 2001
From: Armeen Mahdian <mahdianarmeen@gmail.com>
Date: Fri, 18 Mar 2022 10:03:50 -0500
Subject: [PATCH 07/32] eggnog-mapper: 1.0.3 -> 2.1.7

https://github.com/eggnogdb/eggnog-mapper/releases
---
 .../science/biology/eggnog-mapper/default.nix | 46 ++++++++++++-------
 1 file changed, 30 insertions(+), 16 deletions(-)

diff --git a/pkgs/applications/science/biology/eggnog-mapper/default.nix b/pkgs/applications/science/biology/eggnog-mapper/default.nix
index b42fed8da28..44caca2fa2c 100644
--- a/pkgs/applications/science/biology/eggnog-mapper/default.nix
+++ b/pkgs/applications/science/biology/eggnog-mapper/default.nix
@@ -1,29 +1,43 @@
-{ lib, fetchFromGitHub, fetchpatch, makeWrapper, python27Packages, wget, diamond, hmmer }:
+{ lib
+, autoPatchelfHook
+, fetchFromGitHub
+, python3Packages
+, wget
+, zlib
+}:
 
-python27Packages.buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "eggnog-mapper";
-  version = "1.0.3";
+  version = "2.1.7";
 
   src = fetchFromGitHub {
     owner = "eggnogdb";
-    repo = "eggnog-mapper";
+    repo = pname;
     rev = version;
-    sha256 = "1aaaflppy84bhkh2hb5gnzm4xgrz0rz0cgfpadr9w8cva8p0sqdv";
+    hash = "sha256-auVD/r8m3TAB1KYMQ7Sae23eDg6LRx/daae0505cjwU=";
   };
 
-  patches = (fetchpatch {
-    url = "https://github.com/eggnogdb/eggnog-mapper/commit/6972f601ade85b65090efca747d2302acb58507f.patch";
-    sha256 = "0abnmn0bh11jihf5d3cggiild1ykawzv5f5fhb4cyyi8fvy4hcxf";
-  });
+  postPatch = ''
+    # Not a great solution...
+    substituteInPlace setup.cfg \
+      --replace "==" ">="
+  '';
 
-  nativeBuildInputs = [ makeWrapper ];
-  propagatedBuildInputs = [ python27Packages.biopython wget diamond hmmer ];
+  nativeBuildInputs = [
+    autoPatchelfHook
+  ];
 
-  # make emapper find diamond & hmmer
-  makeWrapperArgs = [
-    ''--prefix PATH ':' "${diamond}/bin"''
-    ''--prefix PATH ':' "${hmmer}/bin"''
-    ];
+  buildInputs = [
+    zlib
+  ];
+
+  propagatedBuildInputs = [
+    wget
+  ] ++ (with python3Packages; [
+    biopython
+    psutil
+    XlsxWriter
+  ]);
 
   # Tests rely on some of the databases being available, which is not bundled
   # with this package as (1) in total, they represent >100GB of data, and (2)

From 99984987a8c570a0beb26400efe3c7ed2628edc0 Mon Sep 17 00:00:00 2001
From: Anatolii Prylutskyi <anpryl@gmail.com>
Date: Sun, 27 Mar 2022 13:23:04 +0300
Subject: [PATCH 08/32] dragon-drop: remove duplicate package

Removing package because it is duplicate package of "xdragon".
---
 pkgs/tools/X11/dragon-drop/default.nix | 28 --------------------------
 pkgs/top-level/all-packages.nix        |  4 +---
 2 files changed, 1 insertion(+), 31 deletions(-)
 delete mode 100644 pkgs/tools/X11/dragon-drop/default.nix

diff --git a/pkgs/tools/X11/dragon-drop/default.nix b/pkgs/tools/X11/dragon-drop/default.nix
deleted file mode 100644
index adf43ae8c08..00000000000
--- a/pkgs/tools/X11/dragon-drop/default.nix
+++ /dev/null
@@ -1,28 +0,0 @@
-{ lib, stdenv, gtk, pkg-config, fetchFromGitHub }:
-
-stdenv.mkDerivation rec {
-  pname = "dragon-drop";
-  version = "1.1.1";
-
-  src = fetchFromGitHub {
-    owner = "mwh";
-    repo = "dragon";
-    rev = "v${version}";
-    sha256 = "0fgzz39007fdjwq72scp0qygp2v3zc5f1xkm0sxaa8zxm25g1bra";
-  };
-
-  nativeBuildInputs = [ pkg-config ];
-  buildInputs = [ gtk ];
-
-  installPhase = ''
-    install -D dragon -t $out/bin
-  '';
-
-  meta = with lib; {
-    description = "Simple drag-and-drop source/sink for X";
-    homepage = "https://github.com/mwh/dragon";
-    maintainers = with maintainers; [ jb55 markus1189 ];
-    license = licenses.gpl3;
-    platforms = with platforms; unix;
-  };
-}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 69e0f05c77b..b29994d3a57 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -2982,9 +2982,7 @@ with pkgs;
 
   dpic = callPackage ../tools/graphics/dpic { };
 
-  dragon-drop = callPackage ../tools/X11/dragon-drop {
-    gtk = gtk3;
-  };
+  dragon-drop = throw "'dragon-drop' has been renamed to/replaced by 'xdragon'"; # Converted to throw 2022-03-27;
 
   dstp = callPackage ../development/tools/dstp { };
 

From 0881f01c5b1f1e7fd613b36880f89b379879b856 Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Wed, 30 Mar 2022 20:39:03 +0200
Subject: [PATCH 09/32] dhcp: 4.4.2-P1 -> 4.4.3

https://downloads.isc.org/isc/dhcp/4.4.3/dhcp-4.4.3-RELNOTES
---
 pkgs/tools/networking/dhcp/default.nix | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/pkgs/tools/networking/dhcp/default.nix b/pkgs/tools/networking/dhcp/default.nix
index 10418d97810..b2d33d0fe3e 100644
--- a/pkgs/tools/networking/dhcp/default.nix
+++ b/pkgs/tools/networking/dhcp/default.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   pname = "dhcp";
-  version = "4.4.2-P1";
+  version = "4.4.3";
 
   src = fetchurl {
     url = "https://ftp.isc.org/isc/dhcp/${version}/${pname}-${version}.tar.gz";
-    sha256 = "06jsr0cg5rsmyibshrpcb9za0qgwvqccashdma7mlm1rflrh8pmh";
+    sha256 = "sha256-Dj7GtMKgXsAUiHS82ZmmbQVRg3jXdCH2B/sLydATWBg=";
   };
 
   patches =
@@ -18,20 +18,6 @@ stdenv.mkDerivation rec {
       # patch, the hostname doesn't get set properly if the old
       # hostname (i.e. before reboot) is equal to the new hostname.
       ./set-hostname.patch
-
-      (fetchpatch {
-        # upstream build fix against -fno-common compilers like >=gcc-10
-        url = "https://gitlab.isc.org/isc-projects/dhcp/-/commit/6c7e61578b1b449272dbb40dd8b98d03dad8a57a.patch";
-        sha256 = "1g37ix0yf9zza8ri8bg438ygcjviniblfyb20y4gzc8lysy28m8b";
-      })
-
-      # Fix parallel build failure, the patch is pending upstream inclusion:
-      #  https://gitlab.isc.org/isc-projects/dhcp/-/merge_requests/76
-      (fetchpatch {
-        name = "parallel-make.patch";
-        url = "https://gitlab.isc.org/isc-projects/dhcp/-/commit/46d101b97c5a3b19a3f63f7b60e5f88994a64e22.patch";
-        sha256 = "1y3nsmqjzcg4bhp1xmqp47v7rkl3bpcildkx6mlrg255yvxapmdp";
-      })
     ];
 
   nativeBuildInputs = [ perl makeWrapper ];

From a2c379d4b6df39bb5a0355bb4bb68cc3f75f4cc7 Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Wed, 30 Mar 2022 20:39:55 +0200
Subject: [PATCH 10/32] dhcp: make client and relay component optional

and mark the package with knownVulnerabilities when they are enabled.

Closes: #163472
---
 pkgs/tools/networking/dhcp/default.nix | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/pkgs/tools/networking/dhcp/default.nix b/pkgs/tools/networking/dhcp/default.nix
index b2d33d0fe3e..1d1a01d17cf 100644
--- a/pkgs/tools/networking/dhcp/default.nix
+++ b/pkgs/tools/networking/dhcp/default.nix
@@ -1,6 +1,10 @@
 { stdenv, fetchurl, fetchpatch, perl, file, nettools, iputils, iproute2, makeWrapper
 , coreutils, gnused, openldap ? null
 , buildPackages, lib
+
+# client and relay are end of life, remove after 4.4.3
+, withClient ? false
+, withRelay ? false
 }:
 
 stdenv.mkDerivation rec {
@@ -63,6 +67,10 @@ stdenv.mkDerivation rec {
         --replace /sbin/ip ${iproute2}/sbin/ip
       wrapProgram "$out/sbin/dhclient-script" --prefix PATH : \
         "${nettools}/bin:${nettools}/sbin:${iputils}/bin:${coreutils}/bin:${gnused}/bin"
+    '' + lib.optionalString (!withClient) ''
+      rm $out/sbin/{dhclient,dhclient-script,.dhclient-script-wrapped}
+    '' + lib.optionalString (!withRelay) ''
+      rm $out/sbin/dhcrelay
     '';
 
   preConfigure =
@@ -89,5 +97,6 @@ stdenv.mkDerivation rec {
     homepage = "https://www.isc.org/dhcp/";
     license = licenses.mpl20;
     platforms = platforms.unix;
+    knownVulnerabilities = lib.optional (withClient || withRelay) "The client and relay component of the dhcp package have reached their end of life";
   };
 }

From a31f123c1cb68e107f54d1a54500de6ba8b9b0ef Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Wed, 30 Mar 2022 20:43:16 +0200
Subject: [PATCH 11/32] networkmanager: remove dhcp and pass dhcpcd instead

The ISC DHCP client has reached its end of life.
---
 nixos/modules/services/networking/networkmanager.nix | 3 +--
 pkgs/tools/networking/networkmanager/default.nix     | 8 ++++----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/nixos/modules/services/networking/networkmanager.nix b/nixos/modules/services/networking/networkmanager.nix
index 7a9d9e5428a..f14eea50ada 100644
--- a/nixos/modules/services/networking/networkmanager.nix
+++ b/nixos/modules/services/networking/networkmanager.nix
@@ -237,7 +237,7 @@ in {
       };
 
       dhcp = mkOption {
-        type = types.enum [ "dhclient" "dhcpcd" "internal" ];
+        type = types.enum [ "dhcpcd" "internal" ];
         default = "internal";
         description = ''
           Which program (or internal library) should be used for DHCP.
@@ -497,7 +497,6 @@ in {
       "d /etc/ipsec.d 0700 root root -"
       "d /var/lib/NetworkManager-fortisslvpn 0700 root root -"
 
-      "d /var/lib/dhclient 0755 root root -"
       "d /var/lib/misc 0755 root root -" # for dnsmasq.leases
     ];
 
diff --git a/pkgs/tools/networking/networkmanager/default.nix b/pkgs/tools/networking/networkmanager/default.nix
index 2c984da8737..86195ba8692 100644
--- a/pkgs/tools/networking/networkmanager/default.nix
+++ b/pkgs/tools/networking/networkmanager/default.nix
@@ -12,7 +12,7 @@
 , polkit
 , gnutls
 , ppp
-, dhcp
+, dhcpcd
 , iptables
 , nftables
 , python3
@@ -96,9 +96,9 @@ stdenv.mkDerivation rec {
     "-Dresolvconf=${openresolv}/bin/resolvconf"
 
     # DHCP clients
-    "-Ddhclient=${dhcp}/bin/dhclient"
-    # Upstream prefers dhclient, so don't add dhcpcd to the closure
-    "-Ddhcpcd=no"
+    # ISC DHCP client has reached it's end of life, so stop using it
+    "-Ddhclient=no"
+    "-Ddhcpcd=${dhcpcd}/bin/dhcpcd"
     "-Ddhcpcanon=no"
 
     # Miscellaneous

From c6e3a81aea61b7e12560e1b346d285f90b70274d Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Wed, 30 Mar 2022 20:49:30 +0200
Subject: [PATCH 12/32] pipework: remove dhcp package

Pipework can optionally use dhclient, but supports other dhcp clients as
well, so we can safely remove it.
---
 pkgs/os-specific/linux/pipework/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/os-specific/linux/pipework/default.nix b/pkgs/os-specific/linux/pipework/default.nix
index 33192392888..ea274377ced 100644
--- a/pkgs/os-specific/linux/pipework/default.nix
+++ b/pkgs/os-specific/linux/pipework/default.nix
@@ -1,5 +1,5 @@
 { stdenv, lib, fetchFromGitHub, makeWrapper
-, bridge-utils, iproute2, lxc, openvswitch, docker, busybox, dhcpcd, dhcp
+, bridge-utils, iproute2, lxc, openvswitch, docker, busybox, dhcpcd
 }:
 
 stdenv.mkDerivation {
@@ -15,7 +15,7 @@ stdenv.mkDerivation {
   installPhase = ''
     install -D pipework $out/bin/pipework
     wrapProgram $out/bin/pipework --prefix PATH : \
-      ${lib.makeBinPath [ bridge-utils iproute2 lxc openvswitch docker busybox dhcpcd dhcp ]};
+      ${lib.makeBinPath [ bridge-utils iproute2 lxc openvswitch docker busybox dhcpcd ]};
   '';
   meta = with lib; {
     description = "Software-Defined Networking tools for LXC";

From 84d6565d52d1f9f25280f8dc1716b90238fbb738 Mon Sep 17 00:00:00 2001
From: Jan Tojnar <jtojnar@gmail.com>
Date: Thu, 31 Mar 2022 02:34:42 +0200
Subject: [PATCH 13/32] nixos/man: prevent duplication of options
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

libxslt 1.1.35 fixed conflict resolution for templates to match the specification.
This uncovered a bug in docbook-xsl (https://github.com/docbook/xslt10-stylesheets/issues/240),
which causes option names to be duplicated into the option descriptions.

Let’s resolve the conflict by patching the stylesheets.

Fixes: https://github.com/NixOS/nixpkgs/issues/166304
---
 nixos/doc/manual/default.nix                          |  4 ++++
 .../sgml+xml/stylesheets/xslt/docbook-xsl/default.nix |  6 +++++-
 .../docbook-xsl/fix-man-options-duplication.patch     | 11 +++++++++++
 3 files changed, 20 insertions(+), 1 deletion(-)
 create mode 100644 pkgs/data/sgml+xml/stylesheets/xslt/docbook-xsl/fix-man-options-duplication.patch

diff --git a/nixos/doc/manual/default.nix b/nixos/doc/manual/default.nix
index e96bc47b4a5..bcb5d0d02f7 100644
--- a/nixos/doc/manual/default.nix
+++ b/nixos/doc/manual/default.nix
@@ -14,6 +14,10 @@ with pkgs;
 let
   lib = pkgs.lib;
 
+  docbook_xsl_ns = pkgs.docbook-xsl-ns.override {
+    withManOptDedupPatch = true;
+  };
+
   # We need to strip references to /nix/store/* from options,
   # including any `extraSources` if some modules came from elsewhere,
   # or else the build will fail.
diff --git a/pkgs/data/sgml+xml/stylesheets/xslt/docbook-xsl/default.nix b/pkgs/data/sgml+xml/stylesheets/xslt/docbook-xsl/default.nix
index 735dfdb4f81..2f9d22e57d8 100644
--- a/pkgs/data/sgml+xml/stylesheets/xslt/docbook-xsl/default.nix
+++ b/pkgs/data/sgml+xml/stylesheets/xslt/docbook-xsl/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, substituteAll, fetchurl, fetchpatch, findXMLCatalogs, writeScriptBin, ruby, bash }:
+{ lib, stdenv, substituteAll, fetchurl, fetchpatch, findXMLCatalogs, writeScriptBin, ruby, bash, withManOptDedupPatch ? false }:
 
 let
 
@@ -36,6 +36,10 @@ let
           src = ./catalog-legacy-uris.patch;
           inherit legacySuffix suffix version;
         })
+      ] ++ lib.optionals withManOptDedupPatch [
+        # Fixes https://github.com/NixOS/nixpkgs/issues/166304
+        # https://github.com/docbook/xslt10-stylesheets/pull/241
+        ./fix-man-options-duplication.patch
       ];
 
       propagatedBuildInputs = [ findXMLCatalogs ];
diff --git a/pkgs/data/sgml+xml/stylesheets/xslt/docbook-xsl/fix-man-options-duplication.patch b/pkgs/data/sgml+xml/stylesheets/xslt/docbook-xsl/fix-man-options-duplication.patch
new file mode 100644
index 00000000000..304d9781e6a
--- /dev/null
+++ b/pkgs/data/sgml+xml/stylesheets/xslt/docbook-xsl/fix-man-options-duplication.patch
@@ -0,0 +1,11 @@
+--- a/manpages/lists.xsl
++++ b/manpages/lists.xsl
+@@ -110,7 +110,7 @@
+   <xsl:text>.RE&#10;</xsl:text>
+ </xsl:template>
+ 
+-<xsl:template match="d:varlistentry/d:term"/>
++<xsl:template match="d:varlistentry/d:term" priority="1"/>
+ <xsl:template match="d:glossentry/d:glossterm"/>
+ 
+ <xsl:template match="d:variablelist[ancestor::d:listitem or ancestor::d:step or ancestor::d:glossdef]|

From c4d4de89ddac3e11f4c0e4b3c9f6bd074796cbb3 Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Fri, 8 Apr 2022 00:38:35 +0200
Subject: [PATCH 14/32] gzip: 1.11 -> 1.12

https://savannah.gnu.org/forum/forum.php?forum_id=10157
https://git.savannah.gnu.org/cgit/gzip.git/commit/?id=dc9740df61e575e8c3148b7bd3c147a81ea00c7c

Fixes: CVE-2022-1271
---
 pkgs/tools/compression/gzip/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/compression/gzip/default.nix b/pkgs/tools/compression/gzip/default.nix
index 8bec5b481c9..bd28ca63e80 100644
--- a/pkgs/tools/compression/gzip/default.nix
+++ b/pkgs/tools/compression/gzip/default.nix
@@ -11,11 +11,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gzip";
-  version = "1.11";
+  version = "1.12";
 
   src = fetchurl {
     url = "mirror://gnu/gzip/${pname}-${version}.tar.xz";
-    sha256 = "01vrly90rvc98af6rcmrb3gwv1l6pylasvsdka23dffwizb9b6lv";
+    sha256 = "sha256-zl4D5Rn2N+H4FAEazjXE+HszwLur7sNbr1+9NHnpGVY=";
   };
 
   outputs = [ "out" "man" "info" ];

From e3d9b2115958472d51298d1653f90f993acd3eba Mon Sep 17 00:00:00 2001
From: Rick van Schijndel <rol3517@gmail.com>
Date: Tue, 5 Apr 2022 21:51:32 +0200
Subject: [PATCH 15/32] zlib: fix cross-compilation not producing shared
 libraries

Apply patch that already has been applied upstream:
- https://github.com/madler/zlib/pull/607
- https://github.com/madler/zlib/commit/05796d3d8d5546cf1b4dfe2cd72ab746afae505d

(cherry picked from commit f091c0e80dd2b8b4323fec041068c77b1a5c48f2)
---
 pkgs/development/libraries/zlib/default.nix   |  4 ++++
 .../zlib/fix-configure-issue-cross.patch      | 24 +++++++++++++++++++
 2 files changed, 28 insertions(+)
 create mode 100644 pkgs/development/libraries/zlib/fix-configure-issue-cross.patch

diff --git a/pkgs/development/libraries/zlib/default.nix b/pkgs/development/libraries/zlib/default.nix
index 91cd037e0e3..9b9938746ca 100644
--- a/pkgs/development/libraries/zlib/default.nix
+++ b/pkgs/development/libraries/zlib/default.nix
@@ -40,6 +40,10 @@ stdenv.mkDerivation (rec {
       --replace 'ARFLAGS="-o"' 'ARFLAGS="-r"'
   '';
 
+  patches = [
+    ./fix-configure-issue-cross.patch
+  ];
+
   outputs = [ "out" "dev" ]
     ++ lib.optional splitStaticOutput "static";
   setOutputFlags = false;
diff --git a/pkgs/development/libraries/zlib/fix-configure-issue-cross.patch b/pkgs/development/libraries/zlib/fix-configure-issue-cross.patch
new file mode 100644
index 00000000000..0136071eabe
--- /dev/null
+++ b/pkgs/development/libraries/zlib/fix-configure-issue-cross.patch
@@ -0,0 +1,24 @@
+From 05796d3d8d5546cf1b4dfe2cd72ab746afae505d Mon Sep 17 00:00:00 2001
+From: Mark Adler <madler@alumni.caltech.edu>
+Date: Mon, 28 Mar 2022 18:34:10 -0700
+Subject: [PATCH] Fix configure issue that discarded provided CC definition.
+
+---
+ configure | 3 +++
+ 1 file changed, 3 insertions(+)
+
+diff --git a/configure b/configure
+index 52ff4a04e..3fa3e8618 100755
+--- a/configure
++++ b/configure
+@@ -174,7 +174,10 @@ if test -z "$CC"; then
+   else
+     cc=${CROSS_PREFIX}cc
+   fi
++else
++  cc=${CC}
+ fi
++
+ cflags=${CFLAGS-"-O3"}
+ # to force the asm version use: CFLAGS="-O3 -DASMV" ./configure
+ case "$cc" in

From befb10cd43d8b905c0fe61e878acd0856eee06cc Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Fri, 8 Apr 2022 21:30:02 +0000
Subject: [PATCH 16/32] pgbouncer: 1.16.1 -> 1.17.0

---
 pkgs/servers/sql/pgbouncer/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/servers/sql/pgbouncer/default.nix b/pkgs/servers/sql/pgbouncer/default.nix
index 441b99c7bcd..0a6bfda03a7 100644
--- a/pkgs/servers/sql/pgbouncer/default.nix
+++ b/pkgs/servers/sql/pgbouncer/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "pgbouncer";
-  version = "1.16.1";
+  version = "1.17.0";
 
   src = fetchurl {
     url = "https://pgbouncer.github.io/downloads/files/${version}/${pname}-${version}.tar.gz";
-    sha256 = "1z7p3ghpmbp5qv1bz9s186jn0hfnr300dc5p0hmh6vbnwklpfx08";
+    sha256 = "sha256-ZXMJt7xceoXL9wqaRBtTX3gkEjCB6rt7qG0ANJolbiM=";
   };
 
   nativeBuildInputs = [ pkg-config ];

From 76492d0c26aa6a2f22dd34557f060b40cc01dc4d Mon Sep 17 00:00:00 2001
From: rnhmjoj <rnhmjoj@inventati.org>
Date: Sat, 9 Apr 2022 04:17:27 +0200
Subject: [PATCH 17/32] leveldb: fix static building

1. The Makefile is long gone and the patch in not needed anymore.

2. For some reason LEVELDB_BUILD_BENCHMARKS=OFF is necessary
   when building statically. (Note: this has always been of
   for the shared build)
---
 pkgs/development/libraries/leveldb/default.nix | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/pkgs/development/libraries/leveldb/default.nix b/pkgs/development/libraries/leveldb/default.nix
index c29a3232727..a6f75413c91 100644
--- a/pkgs/development/libraries/leveldb/default.nix
+++ b/pkgs/development/libraries/leveldb/default.nix
@@ -38,13 +38,9 @@ stdenv.mkDerivation rec {
     "-DBUILD_SHARED_LIBS=${if static then "OFF" else "ON"}"
     "-DCMAKE_SKIP_BUILD_RPATH=OFF"
     "-DLEVELDB_BUILD_TESTS=OFF"
+    "-DLEVELDB_BUILD_BENCHMARKS=OFF"
   ];
 
-  postPatch = lib.optionalString stdenv.hostPlatform.isStatic ''
-    # remove shared objects from "all" target
-    sed -i '/^all:/ s/$(SHARED_LIBS) $(SHARED_PROGRAMS)//' Makefile
-  '';
-
   postInstall = ''
     substituteInPlace "$out"/lib/cmake/leveldb/leveldbTargets.cmake \
       --replace 'INTERFACE_INCLUDE_DIRECTORIES "''${_IMPORT_PREFIX}/include"' 'INTERFACE_INCLUDE_DIRECTORIES "'$dev'"'

From ffaa19174ec3494a8933b0ef10bce50b5e358817 Mon Sep 17 00:00:00 2001
From: Aaron Jheng <wentworth@outlook.com>
Date: Sat, 9 Apr 2022 12:25:47 +0000
Subject: [PATCH 18/32] git-sizer: 1.3.0 -> 1.5.0

---
 .../version-management/git-sizer/default.nix  | 21 +++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/pkgs/applications/version-management/git-sizer/default.nix b/pkgs/applications/version-management/git-sizer/default.nix
index 049a2aa2c1d..daabe71bebb 100644
--- a/pkgs/applications/version-management/git-sizer/default.nix
+++ b/pkgs/applications/version-management/git-sizer/default.nix
@@ -1,20 +1,29 @@
-{ lib, buildGoPackage, fetchFromGitHub }:
+{ lib, buildGoModule, fetchFromGitHub, testVersion, git-sizer }:
 
-buildGoPackage rec {
+buildGoModule rec {
   pname = "git-sizer";
-  version = "1.3.0";
-
-  goPackagePath = "github.com/github/git-sizer";
+  version = "1.5.0";
 
   src = fetchFromGitHub {
     owner = "github";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0kmyvai5xfalm56ywa6mhdvvjnacdzwcyz28bw0pz9a4gyf1mgvh";
+    sha256 = "sha256-On7QBTzKfnuuzwMQ8m1odxGqfIKL+EDg5V05Kxuhmqw=";
+  };
+
+  vendorSha256 = "sha256-oRlsD99XiI/0ZWibjyRcycmGab+vMbXrV5hIdIyUDYg=";
+
+  ldflags = [ "-s" "-w" "-X main.BuildVersion=${version}" ];
+
+  doCheck = false;
+
+  passthru.tests.vesion = testVersion {
+    package = git-sizer;
   };
 
   meta = with lib; {
     description = "Compute various size metrics for a Git repository";
+    homepage = "https://github.com/github/git-sizer";
     license = licenses.mit;
     maintainers = with maintainers; [ matthewbauer ];
   };

From 0fad2b34c4e1454ce83ec1486725771273c7c0dc Mon Sep 17 00:00:00 2001
From: Paul Grandperrin <paul.grandperrin@gmail.com>
Date: Sat, 9 Apr 2022 14:50:18 +0200
Subject: [PATCH 19/32] Patch curl certificate CN verification

From https://github.com/curl/curl/commit/911714d617c106ed5d553bf003e34ec94ab6a136
Fixes https://github.com/NixOS/nixpkgs/issues/167971
---
 .../curl/7.82.0-openssl-fix-CN-check.patch    | 30 +++++++++++++++++++
 pkgs/tools/networking/curl/default.nix        |  1 +
 2 files changed, 31 insertions(+)
 create mode 100644 pkgs/tools/networking/curl/7.82.0-openssl-fix-CN-check.patch

diff --git a/pkgs/tools/networking/curl/7.82.0-openssl-fix-CN-check.patch b/pkgs/tools/networking/curl/7.82.0-openssl-fix-CN-check.patch
new file mode 100644
index 00000000000..5d84f512499
--- /dev/null
+++ b/pkgs/tools/networking/curl/7.82.0-openssl-fix-CN-check.patch
@@ -0,0 +1,30 @@
+From 911714d617c106ed5d553bf003e34ec94ab6a136 Mon Sep 17 00:00:00 2001
+From: Daniel Stenberg <daniel@haxx.se>
+Date: Tue, 8 Mar 2022 13:38:13 +0100
+Subject: [PATCH] openssl: fix CN check error code
+
+Due to a missing 'else' this returns error too easily.
+
+Regressed in: d15692ebb
+
+Reported-by: Kristoffer Gleditsch
+Fixes #8559
+Closes #8560
+---
+ lib/vtls/openssl.c | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/lib/vtls/openssl.c b/lib/vtls/openssl.c
+index 0b79fc50a9c5..4618beeb3867 100644
+--- a/lib/vtls/openssl.c
++++ b/lib/vtls/openssl.c
+@@ -1817,7 +1817,8 @@ CURLcode Curl_ossl_verifyhost(struct Curl_easy *data, struct connectdata *conn,
+               memcpy(peer_CN, ASN1_STRING_get0_data(tmp), peerlen);
+               peer_CN[peerlen] = '\0';
+             }
+-            result = CURLE_OUT_OF_MEMORY;
++            else
++              result = CURLE_OUT_OF_MEMORY;
+           }
+         }
+         else /* not a UTF8 name */
diff --git a/pkgs/tools/networking/curl/default.nix b/pkgs/tools/networking/curl/default.nix
index c032ba61c12..a7cac48d52d 100644
--- a/pkgs/tools/networking/curl/default.nix
+++ b/pkgs/tools/networking/curl/default.nix
@@ -66,6 +66,7 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./7.79.1-darwin-no-systemconfiguration.patch
+    ./7.82.0-openssl-fix-CN-check.patch
   ];
 
   outputs = [ "bin" "dev" "out" "man" "devdoc" ];

From dc508e7f5af09a01abdb41cdf580cd151ade72f2 Mon Sep 17 00:00:00 2001
From: Ilya Fedin <fedin-ilja2010@ya.ru>
Date: Sun, 10 Apr 2022 01:35:55 +0400
Subject: [PATCH 20/32] kotatogram-desktop-with-webkit: init

This allows to get maximum from the dlopen-based code and install webkit dependency only when needed and without rebuilds

Tested with https://t.me/ShopBot
---
 .../telegram/kotatogram-desktop/default.nix   | 21 -----------------
 .../kotatogram-desktop/with-webkit.nix        | 23 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 3 files changed, 25 insertions(+), 21 deletions(-)
 create mode 100644 pkgs/applications/networking/instant-messengers/telegram/kotatogram-desktop/with-webkit.nix

diff --git a/pkgs/applications/networking/instant-messengers/telegram/kotatogram-desktop/default.nix b/pkgs/applications/networking/instant-messengers/telegram/kotatogram-desktop/default.nix
index ce5dc0e266e..f46a918d3c6 100644
--- a/pkgs/applications/networking/instant-messengers/telegram/kotatogram-desktop/default.nix
+++ b/pkgs/applications/networking/instant-messengers/telegram/kotatogram-desktop/default.nix
@@ -7,7 +7,6 @@
 , ninja
 , clang
 , python3
-, wrapGAppsHook
 , wrapQtAppsHook
 , removeReferencesTo
 , extra-cmake-modules
@@ -27,7 +26,6 @@
 , tl-expected
 , hunspell
 , glibmm
-, webkitgtk
 , jemalloc
 , rnnoise
 , abseil-cpp
@@ -65,7 +63,6 @@
 , IOSurface
 , Metal
 , MetalKit
-, withWebKit ? false
 }:
 
 with lib;
@@ -113,9 +110,6 @@ stdenv.mkDerivation rec {
       --replace '"libasound.so.2"' '"${alsa-lib}/lib/libasound.so.2"'
     substituteInPlace Telegram/ThirdParty/libtgvoip/os/linux/AudioPulse.cpp \
       --replace '"libpulse.so.0"' '"${libpulseaudio}/lib/libpulse.so.0"'
-  '' + optionalString (stdenv.isLinux && withWebKit) ''
-    substituteInPlace Telegram/lib_webview/webview/platform/linux/webview_linux_webkit_gtk.cpp \
-      --replace '"libwebkit2gtk-4.0.so.37"' '"${webkitgtk}/lib/libwebkit2gtk-4.0.so.37"'
   '' + optionalString stdenv.isDarwin ''
     substituteInPlace Telegram/CMakeLists.txt \
       --replace 'COMMAND iconutil' 'COMMAND png2icns' \
@@ -124,10 +118,6 @@ stdenv.mkDerivation rec {
       --replace "\''${appicon_path}" "\''${appicon_path}/icon_16x16.png \''${appicon_path}/icon_32x32.png \''${appicon_path}/icon_128x128.png \''${appicon_path}/icon_256x256.png \''${appicon_path}/icon_512x512.png"
   '';
 
-  # We want to run wrapProgram manually (with additional parameters)
-  dontWrapGApps = stdenv.isLinux;
-  dontWrapQtApps = stdenv.isLinux && withWebKit;
-
   nativeBuildInputs = [
     pkg-config
     cmake
@@ -139,8 +129,6 @@ stdenv.mkDerivation rec {
     # to build bundled libdispatch
     clang
     extra-cmake-modules
-  ] ++ optionals (stdenv.isLinux && withWebKit) [
-    wrapGAppsHook
   ];
 
   buildInputs = [
@@ -166,8 +154,6 @@ stdenv.mkDerivation rec {
     glibmm
     jemalloc
     wayland
-  ] ++ optionals (stdenv.isLinux && withWebKit) [
-    webkitgtk
   ] ++ optionals stdenv.isDarwin [
     Cocoa
     CoreFoundation
@@ -225,13 +211,6 @@ stdenv.mkDerivation rec {
     remove-references-to -t ${tg_owt.dev} $out/bin/$binName
   '';
 
-  postFixup = optionalString (stdenv.isLinux && withWebKit) ''
-    # We also use gappsWrapperArgs from wrapGAppsHook.
-    wrapProgram $out/bin/kotatogram-desktop \
-      "''${gappsWrapperArgs[@]}" \
-      "''${qtWrapperArgs[@]}"
-  '';
-
   passthru = {
     inherit tg_owt;
   };
diff --git a/pkgs/applications/networking/instant-messengers/telegram/kotatogram-desktop/with-webkit.nix b/pkgs/applications/networking/instant-messengers/telegram/kotatogram-desktop/with-webkit.nix
new file mode 100644
index 00000000000..435268cdf62
--- /dev/null
+++ b/pkgs/applications/networking/instant-messengers/telegram/kotatogram-desktop/with-webkit.nix
@@ -0,0 +1,23 @@
+{ stdenv, lib, kotatogram-desktop, glib-networking, webkitgtk, makeWrapper }:
+
+with lib;
+
+stdenv.mkDerivation {
+  pname = "${kotatogram-desktop.pname}-with-webkit";
+  version = kotatogram-desktop.version;
+  nativeBuildInputs = [ makeWrapper ];
+  dontUnpack = true;
+  installPhase = ''
+    mkdir -p $out
+    cp -r ${kotatogram-desktop}/share $out
+  '';
+  postFixup = ''
+    mkdir -p $out/bin
+    makeWrapper ${kotatogram-desktop}/bin/kotatogram-desktop $out/bin/kotatogram-desktop \
+      --prefix GIO_EXTRA_MODULES : ${glib-networking}/lib/gio/modules \
+      --prefix LD_LIBRARY_PATH : ${makeLibraryPath [ webkitgtk ]}
+  '';
+  meta = kotatogram-desktop.meta // {
+    platforms = platforms.linux;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b746e502f24..78aeb1257ec 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -27058,6 +27058,8 @@ with pkgs;
     abseil-cpp = abseil-cpp_202111;
   };
 
+  kotatogram-desktop-with-webkit = callPackage ../applications/networking/instant-messengers/telegram/kotatogram-desktop/with-webkit.nix {};
+
   kpt = callPackage ../applications/networking/cluster/kpt { };
 
   krane = callPackage ../applications/networking/cluster/krane { };

From 2fd4f690a90a8405073ff040935807ef86a06512 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Sun, 10 Apr 2022 05:36:08 +0000
Subject: [PATCH 21/32] xmedcon: 0.21.2 -> 0.22.0

---
 pkgs/applications/science/medicine/xmedcon/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/medicine/xmedcon/default.nix b/pkgs/applications/science/medicine/xmedcon/default.nix
index bee2be729d1..2050517894b 100644
--- a/pkgs/applications/science/medicine/xmedcon/default.nix
+++ b/pkgs/applications/science/medicine/xmedcon/default.nix
@@ -10,11 +10,11 @@
 
 stdenv.mkDerivation rec {
   pname = "xmedcon";
-  version = "0.21.2";
+  version = "0.22.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/${pname}/${pname}-${version}.tar.bz2";
-    sha256 = "0svff8rc3j2p47snaq1hx9mv4ydmxawpb0hf3d165g1ccjwvmm6m";
+    sha256 = "sha256-Ui7XoLSzTMPIFW/3nARCmvlGF+1l7pmcnKsnvn3NFJE=";
   };
 
   buildInputs = [

From ab3d8bd20ddda39c1a7cb85082560c31bd1e1b66 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Sun, 10 Apr 2022 06:47:06 +0000
Subject: [PATCH 22/32] yed: 3.21.1 -> 3.22

---
 pkgs/applications/graphics/yed/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/graphics/yed/default.nix b/pkgs/applications/graphics/yed/default.nix
index d2873f64142..0385c5db9d8 100644
--- a/pkgs/applications/graphics/yed/default.nix
+++ b/pkgs/applications/graphics/yed/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "yEd";
-  version = "3.21.1";
+  version = "3.22";
 
   src = fetchzip {
     url = "https://www.yworks.com/resources/yed/demo/${pname}-${version}.zip";
-    sha256 = "1jw28hkd7p0n660gid8yh5y0kdcz6ycn4hsgjlf0pq48x9kv6w0c";
+    sha256 = "sha256-GHYdvWie2k9YarS9DaA4bExswV3UQ26O8+7K/6yvtac=";
   };
 
   nativeBuildInputs = [ makeWrapper unzip wrapGAppsHook ];

From 15d1734496e8216083c80dea813653a717f6f20f Mon Sep 17 00:00:00 2001
From: Robert Scott <code@humanleg.org.uk>
Date: Sat, 26 Mar 2022 19:41:29 +0000
Subject: [PATCH 23/32] libtiff: add patches for multiple CVEs

CVE-2022-0891
CVE-2022-0865
CVE-2022-0924
CVE-2022-0907
CVE-2022-0909
CVE-2022-0908

(cherry picked from commit 748dfdd1f58ee07395fbf from PR #165872)
---
 .../development/libraries/libtiff/default.nix | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/pkgs/development/libraries/libtiff/default.nix b/pkgs/development/libraries/libtiff/default.nix
index 19076527340..6b455d992b8 100644
--- a/pkgs/development/libraries/libtiff/default.nix
+++ b/pkgs/development/libraries/libtiff/default.nix
@@ -53,6 +53,36 @@ stdenv.mkDerivation rec {
       url = "https://gitlab.com/libtiff/libtiff/-/commit/561599c99f987dc32ae110370cfdd7df7975586b.patch";
       sha256 = "0ycirjjc1vigj03kwjb92n6jszsl9p17ccw5hry7lli9gxyyr0an";
     })
+    (fetchpatch {
+      name = "CVE-2022-0891.patch";
+      url = "https://gitlab.com/libtiff/libtiff/-/commit/46dc8fcd4d38c3b6f35ab28e532aee80e6f609d6.patch";
+      sha256 = "1zn2pgsmbrjx3g2bpdggvwwbp6i348mikwlx4ws482h2379vmyj1";
+    })
+    (fetchpatch {
+      name = "CVE-2022-0865.patch";
+      url = "https://gitlab.com/libtiff/libtiff/-/commit/5e18004500cda10d9074bdb6166b054e95b659ed.patch";
+      sha256 = "131b9ial6avl2agwk31wp2jkrx59955f4r0dikx1jdaywqb7zhd1";
+    })
+    (fetchpatch {
+      name = "CVE-2022-0924.patch";
+      url = "https://gitlab.com/libtiff/libtiff/-/commit/408976c44ef0aad975e0d1b6c6dc80d60f9dc665.patch";
+      sha256 = "1aqaynp74ijxr3rizvbyz23ncs71pbbcw5src1zv46473sy55s8p";
+    })
+    (fetchpatch {
+      name = "CVE-2022-0907.patch";
+      url = "https://gitlab.com/libtiff/libtiff/-/commit/f2b656e2e64adde07a6cffd5c8e96bd81a850fea.patch";
+      sha256 = "0nsplq671qx0f35qww9mx27raqp3nvslz8iv7f3hxdgldylmh2vs";
+    })
+    (fetchpatch {
+      name = "CVE-2022-0909.patch";
+      url = "https://gitlab.com/libtiff/libtiff/-/commit/f8d0f9aa1ba04c9ae3bfe869a18141a8b8117ad7.patch";
+      sha256 = "1plhk6ildl16bp0k3wvzfd4a97hqfqfbbn7vjinsaasf4v0x3q5j";
+    })
+    (fetchpatch {
+      name = "CVE-2022-0908.patch";
+      url = "https://gitlab.com/libtiff/libtiff/-/commit/a95b799f65064e4ba2e2dfc206808f86faf93e85.patch";
+      sha256 = "0i61kkjaixdn2p933lpma9s6i0772vhxjxxcwyqagw96lmszrcm7";
+    })
   ];
 
   postPatch = ''

From 836d4062517b8c44e6cd506c52f8f205040dd3e6 Mon Sep 17 00:00:00 2001
From: Stig Palmquist <stig@stig.io>
Date: Sun, 3 Apr 2022 22:31:05 +0200
Subject: [PATCH 24/32] perl: use pkgs.zlib instead of bundled zlib

(cherry picked from commit d1adf502779a0 from PR #167084)
---
 pkgs/development/interpreters/perl/default.nix | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/pkgs/development/interpreters/perl/default.nix b/pkgs/development/interpreters/perl/default.nix
index f29e61d1105..81099b96745 100644
--- a/pkgs/development/interpreters/perl/default.nix
+++ b/pkgs/development/interpreters/perl/default.nix
@@ -1,6 +1,7 @@
 { config, lib, stdenv, fetchurl, fetchpatch, fetchFromGitHub, pkgs, buildPackages
 , callPackage
 , enableThreading ? true, coreutils, makeWrapper
+, zlib
 }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
@@ -115,6 +116,16 @@ let
         cf_by="nixpkgs"
         cf_time="$(date -d "@$SOURCE_DATE_EPOCH")"
         EOF
+
+        # Compress::Raw::Zlib should use our zlib package instead of the one
+        # included with the distribution
+        cat > ./cpan/Compress-Raw-Zlib/config.in <<EOF
+        BUILD_ZLIB   = False
+        INCLUDE      = ${zlib.dev}/include
+        LIB          = ${zlib.out}/lib
+        OLD_ZLIB     = False
+        GZIP_OS_CODE = AUTO_DETECT
+        EOF
       '' + optionalString stdenv.isDarwin ''
         substituteInPlace hints/darwin.sh --replace "env MACOSX_DEPLOYMENT_TARGET=10.3" ""
       '' + optionalString (!enableThreading) ''

From 25b43e170f32c4fbbc45a434f5a677aec3a8d3a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sandro=20J=C3=A4ckel?= <sandro.jaeckel@gmail.com>
Date: Wed, 23 Mar 2022 10:07:00 +0100
Subject: [PATCH 25/32] python39Packages.twisted: don't overwrite patchPhase,
 ...

...fix path to tests, update homepage away from their tract

(cherry picked from commit a8b0e20bc36855504 from PR #165414)
---
 pkgs/development/python-modules/twisted/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/twisted/default.nix b/pkgs/development/python-modules/twisted/default.nix
index 4641e4af404..e78d06eb7ba 100644
--- a/pkgs/development/python-modules/twisted/default.nix
+++ b/pkgs/development/python-modules/twisted/default.nix
@@ -31,7 +31,7 @@ buildPythonPackage rec {
 
   # Patch t.p._inotify to point to libc. Without this,
   # twisted.python.runtime.platform.supportsINotify() == False
-  patchPhase = lib.optionalString stdenv.isLinux ''
+  postPatch = lib.optionalString stdenv.isLinux ''
     substituteInPlace src/twisted/python/_inotify.py --replace \
       "ctypes.util.find_library(\"c\")" "'${stdenv.glibc.out}/lib/libc.so.6'"
   '';
@@ -45,13 +45,13 @@ buildPythonPackage rec {
   '';
 
   checkPhase = ''
-    ${python.interpreter} -m unittest discover -s twisted/test
+    ${python.interpreter} -m unittest discover -s src/twisted/test
   '';
   # Tests require network
   doCheck = false;
 
   meta = with lib; {
-    homepage = "https://twistedmatrix.com/";
+    homepage = "https://github.com/twisted/twisted";
     description = "Twisted, an event-driven networking engine written in Python";
     longDescription = ''
       Twisted is an event-driven networking engine written in Python

From 4ba10af21f3581ac7c8eb59ca2e14e88711fc6f9 Mon Sep 17 00:00:00 2001
From: Anatolii Prylutskyi <anpryl@gmail.com>
Date: Sun, 27 Mar 2022 13:24:27 +0300
Subject: [PATCH 26/32] xdragon: refactor

After removing duplicate package "dragon-drop" moving xdragon
to X11 folder.
---
 pkgs/{applications/misc => tools/X11}/xdragon/default.nix | 0
 pkgs/top-level/aliases.nix                                | 1 +
 pkgs/top-level/all-packages.nix                           | 4 +---
 3 files changed, 2 insertions(+), 3 deletions(-)
 rename pkgs/{applications/misc => tools/X11}/xdragon/default.nix (100%)

diff --git a/pkgs/applications/misc/xdragon/default.nix b/pkgs/tools/X11/xdragon/default.nix
similarity index 100%
rename from pkgs/applications/misc/xdragon/default.nix
rename to pkgs/tools/X11/xdragon/default.nix
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index 174d2c72199..02441bc859b 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -273,6 +273,7 @@ mapAliases ({
   dolphinEmuMaster = dolphin-emu-beta; # Added 2021-11-10
   dotnet-netcore = dotnet-runtime; # Added 2021-10-07
   double_conversion = throw "'double_conversion' has been renamed to/replaced by 'double-conversion'"; # Converted to throw 2022-02-22
+  dragon-drop = throw "'dragon-drop' has been removed in favor of 'xdragon'"; # Added 2022-04-10;
   draftsight = throw "draftsight has been removed, no longer available as freeware"; # Added 2020-08-14
   dvb_apps = throw "dvb_apps has been removed"; # Added 2020-11-03
   dwarf_fortress = throw "'dwarf_fortress' has been renamed to/replaced by 'dwarf-fortress'"; # Converted to throw 2022-02-22
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b29994d3a57..24e7795c28f 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -2982,8 +2982,6 @@ with pkgs;
 
   dpic = callPackage ../tools/graphics/dpic { };
 
-  dragon-drop = throw "'dragon-drop' has been renamed to/replaced by 'xdragon'"; # Converted to throw 2022-03-27;
-
   dstp = callPackage ../development/tools/dstp { };
 
   dsvpn = callPackage ../applications/networking/dsvpn { };
@@ -34066,7 +34064,7 @@ with pkgs;
 
   sift = callPackage ../tools/text/sift { };
 
-  xdragon = lowPrio (callPackage ../applications/misc/xdragon { });
+  xdragon = lowPrio (callPackage ../tools/X11/xdragon { });
 
   xlockmore = callPackage ../misc/screensavers/xlockmore { };
 

From 2459b6628f9f2f598e3354a173df245d821a26b8 Mon Sep 17 00:00:00 2001
From: zowoq <59103226+zowoq@users.noreply.github.com>
Date: Wed, 30 Mar 2022 07:41:51 +1000
Subject: [PATCH 27/32] sqlite: 3.38.1 -> 3.38.2

https://www.sqlite.org/releaselog/3_38_2.html
(cherry picked from commit c46c3a55d9a7814467a93f2404e0cc5b2fdf9ca2)
---
 pkgs/development/libraries/sqlite/default.nix | 4 ++--
 pkgs/development/libraries/sqlite/tools.nix   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/libraries/sqlite/default.nix b/pkgs/development/libraries/sqlite/default.nix
index 6cb2eb4b2d1..0d80a83e8ed 100644
--- a/pkgs/development/libraries/sqlite/default.nix
+++ b/pkgs/development/libraries/sqlite/default.nix
@@ -12,13 +12,13 @@ in
 
 stdenv.mkDerivation rec {
   pname = "sqlite${optionalString interactive "-interactive"}";
-  version = "3.38.1";
+  version = "3.38.2";
 
   # nixpkgs-update: no auto update
   # NB! Make sure to update ./tools.nix src (in the same directory).
   src = fetchurl {
     url = "https://sqlite.org/2022/sqlite-autoconf-${archiveVersion version}.tar.gz";
-    sha256 = "sha256-jjqM65eU2Wg5lZDS3fnVwESpfdg9OLlhM2SiReyKL8Q=";
+    sha256 = "sha256-55dKoUMLrWkKXp95pu5chJKtqCadxnWHWtD7dH18raQ=";
   };
 
   outputs = [ "bin" "dev" "out" ];
diff --git a/pkgs/development/libraries/sqlite/tools.nix b/pkgs/development/libraries/sqlite/tools.nix
index 6b07c762881..ebb887ffa01 100644
--- a/pkgs/development/libraries/sqlite/tools.nix
+++ b/pkgs/development/libraries/sqlite/tools.nix
@@ -4,12 +4,12 @@ let
   archiveVersion = import ./archive-version.nix lib;
   mkTool = { pname, makeTarget, description, homepage }: stdenv.mkDerivation rec {
     inherit pname;
-    version = "3.38.1";
+    version = "3.38.2";
 
     # nixpkgs-update: no auto update
     src = assert version == sqlite.version; fetchurl {
       url = "https://sqlite.org/2022/sqlite-src-${archiveVersion version}.zip";
-      sha256 = "sha256-F3rv2oF/qfUoJeF0hYf3wnqbXmtTpIHNQ0YfJ0bZMdg=";
+      sha256 = "sha256-x8DwcKM4yS6wiAWQXAXyVPpG0cTdo1SKAkdPb7VnMpo=";
     };
 
     nativeBuildInputs = [ unzip ];

From 07eeff90551918756ba75586497e02f9dd50f61f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Janne=20He=C3=9F?= <janne@hess.ooo>
Date: Fri, 8 Apr 2022 20:21:53 +0200
Subject: [PATCH 28/32] Merge #167852: openssh: 8.9p1 -> 9.0p1

(cherry picked from commit 830b4daeb1f3f4791e1e4965acaeb910aeaee3d4)
> This release is focused on bug fixing.
---
 pkgs/tools/networking/openssh/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/networking/openssh/default.nix b/pkgs/tools/networking/openssh/default.nix
index 77277f20950..f0063ca832d 100644
--- a/pkgs/tools/networking/openssh/default.nix
+++ b/pkgs/tools/networking/openssh/default.nix
@@ -6,11 +6,11 @@ in
 
   openssh = common rec {
     pname = "openssh";
-    version = "8.9p1";
+    version = "9.0p1";
 
     src = fetchurl {
       url = "mirror://openbsd/OpenSSH/portable/openssh-${version}.tar.gz";
-      sha256 = "sha256:1ry5prcax0134v6srkgznpl9ch5snkgq7yvjqvd8c5mbnxa7cjgx";
+      sha256 = "12m2f9czvgmi7akp7xah6y7mrrpi280a3ksk47iwr7hy2q1475q3";
     };
 
     extraPatches = [ ./ssh-keysign-8.5.patch ];

From 974314755e5afa6a0d38fdbdfe109814e9b521d2 Mon Sep 17 00:00:00 2001
From: Anders Kaseorg <andersk@mit.edu>
Date: Sat, 9 Apr 2022 22:11:57 -0700
Subject: [PATCH 29/32] glibc: Fix segfault in getpwuid when stat fails
 (#167932)

Fixes #167785 using this patch submitted upstream:

https://sourceware.org/bugzilla/show_bug.cgi?id=28752
https://patchwork.sourceware.org/project/glibc/patch/20220314175316.3239120-2-sam@gentoo.org/

(cherry picked from commit a20e363e6b9b00f2adc170883b7204436b449ddf)
---
 pkgs/development/libraries/glibc/common.nix | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/pkgs/development/libraries/glibc/common.nix b/pkgs/development/libraries/glibc/common.nix
index 47aa304e7d3..bf77f6abaa3 100644
--- a/pkgs/development/libraries/glibc/common.nix
+++ b/pkgs/development/libraries/glibc/common.nix
@@ -127,6 +127,13 @@ stdenv.mkDerivation ({
       ./nix-nss-open-files.patch
 
       ./0001-Revert-Remove-all-usage-of-BASH-or-BASH-in-installed.patch
+
+      /* Fix segfault in getpwuid when stat fails
+         https://sourceware.org/bugzilla/show_bug.cgi?id=28752 */
+      (fetchurl {
+        url = "https://patchwork.sourceware.org/project/glibc/patch/20220314175316.3239120-2-sam@gentoo.org/raw/";
+        sha256 = "sq0BoPqXHQ69Vq4zJobCspe4XRfnAiuac/wqzVQJESc=";
+      })
     ]
     ++ lib.optional stdenv.hostPlatform.isMusl ./fix-rpc-types-musl-conflicts.patch
     ++ lib.optional stdenv.buildPlatform.isDarwin ./darwin-cross-build.patch;

From a4e4e497dfe8e1f140569d34e1d14b3b96ab2924 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Sun, 6 Mar 2022 20:32:17 +0000
Subject: [PATCH 30/32] xdragon: 1.1.1 -> 1.2.0

---
 pkgs/tools/X11/xdragon/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/tools/X11/xdragon/default.nix b/pkgs/tools/X11/xdragon/default.nix
index 39f291a8849..7061a8f0a1c 100644
--- a/pkgs/tools/X11/xdragon/default.nix
+++ b/pkgs/tools/X11/xdragon/default.nix
@@ -2,19 +2,19 @@
 
 stdenv.mkDerivation rec {
   pname = "xdragon";
-  version = "1.1.1";
+  version = "1.2.0";
 
   src = fetchFromGitHub {
     owner = "mwh";
     repo = "dragon";
     rev = "v${version}";
-    sha256 = "0fgzz39007fdjwq72scp0qygp2v3zc5f1xkm0sxaa8zxm25g1bra";
+    sha256 = "sha256-wqG6idlVvdN+sPwYgWu3UL0la5ssvymZibiak3KeV7M=";
   };
 
   nativeBuildInputs = [ pkg-config ];
   buildInputs = [ gtk3 ];
 
-  installFlags = [ "PREFIX=${placeholder "out"}/bin" ];
+  installFlags = [ "PREFIX=${placeholder "out"}" ];
   postInstall = ''
     ln -s $out/bin/dragon $out/bin/xdragon
   '';

From af91ac7b0f2a6f8cd0ba4b96b939c026efaa09eb Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Sun, 10 Apr 2022 10:47:59 +0000
Subject: [PATCH 31/32] clj-kondo: 2022.03.09 -> 2022.04.08

---
 pkgs/development/tools/clj-kondo/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/tools/clj-kondo/default.nix b/pkgs/development/tools/clj-kondo/default.nix
index 0a369bd5f03..0268ad463ff 100644
--- a/pkgs/development/tools/clj-kondo/default.nix
+++ b/pkgs/development/tools/clj-kondo/default.nix
@@ -2,11 +2,11 @@
 
 buildGraalvmNativeImage rec {
   pname = "clj-kondo";
-  version = "2022.03.09";
+  version = "2022.04.08";
 
   src = fetchurl {
     url = "https://github.com/clj-kondo/${pname}/releases/download/v${version}/${pname}-${version}-standalone.jar";
-    sha256 = "sha256-gPn3wORb30I/zTXUdxUxMesKFJx6ES7jEjUYuC/DAVI=";
+    sha256 = "sha256-dZtiwePwgLgKc0WkSnxI2zW9hOWKVW5+rO905LQhgvQ=";
   };
 
   extraNativeImageBuildArgs = [

From 24fc4878bcd30929ce6f3964e76cc8746560ec77 Mon Sep 17 00:00:00 2001
From: happysalada <raphael@megzari.com>
Date: Sat, 9 Apr 2022 12:33:50 -0400
Subject: [PATCH 32/32] starship: 1.3.0 -> 1.5.4

---
 pkgs/tools/misc/starship/default.nix | 9 +++++----
 pkgs/top-level/all-packages.nix      | 2 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/pkgs/tools/misc/starship/default.nix b/pkgs/tools/misc/starship/default.nix
index a27674290d6..b595cf10294 100644
--- a/pkgs/tools/misc/starship/default.nix
+++ b/pkgs/tools/misc/starship/default.nix
@@ -9,22 +9,23 @@
 , nixosTests
 , Security
 , Foundation
+, Cocoa
 }:
 
 rustPlatform.buildRustPackage rec {
   pname = "starship";
-  version = "1.3.0";
+  version = "1.5.4";
 
   src = fetchFromGitHub {
     owner = "starship";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-mqUE4JzNBhvtDpT2LM23eHX8q93wtPqA+/zr/PxEDiE=";
+    sha256 = "sha256-nLzqfSRmA+D310MDvX+g8nNsoaiSixG+j+g87CPzYMs=";
   };
 
   nativeBuildInputs = [ installShellFiles pkg-config ];
 
-  buildInputs = [ libgit2 ] ++ lib.optionals stdenv.isDarwin [ libiconv Security Foundation ];
+  buildInputs = [ libgit2 ] ++ lib.optionals stdenv.isDarwin [ libiconv Security Foundation Cocoa ];
 
   postInstall = ''
     for shell in bash fish zsh; do
@@ -33,7 +34,7 @@ rustPlatform.buildRustPackage rec {
     done
   '';
 
-  cargoSha256 = "sha256-hQNDiayVT4UgbxcxdXssi/evPvwgyvG/UOFyEHj7jpo=";
+  cargoSha256 = "sha256-FXzAvO11NIr6dxF2OeV5XJWHG2kgZiASuBnoC6mSps8=";
 
   preCheck = ''
     HOME=$TMPDIR
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 592ce2e63a7..986ff6589c8 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -24294,7 +24294,7 @@ with pkgs;
   stdmanpages = callPackage ../data/documentation/std-man-pages { };
 
   starship = callPackage ../tools/misc/starship {
-    inherit (darwin.apple_sdk.frameworks) Security Foundation;
+    inherit (darwin.apple_sdk.frameworks) Security Foundation Cocoa;
   };
 
   stig = callPackage ../applications/networking/p2p/stig { };