From b155b1dafb52b4b9e352da2da9bf914be29a325a Mon Sep 17 00:00:00 2001
From: CrystalGamma <dev@crystalgamma.de>
Date: Thu, 2 Jul 2020 20:15:08 +0200
Subject: [PATCH 01/55] makeModulesClosure: handle builtin modules better

The previous code discarded entire dependency trees if the first entry in the dependency list compiled by `modprobe --show-depends` is a builtin and otherwise handled its output in a rather hackish way.
---
 pkgs/build-support/kernel/modules-closure.sh | 67 +++++++++++++-------
 1 file changed, 43 insertions(+), 24 deletions(-)

diff --git a/pkgs/build-support/kernel/modules-closure.sh b/pkgs/build-support/kernel/modules-closure.sh
index 220f3b00a771..68d840f16140 100644
--- a/pkgs/build-support/kernel/modules-closure.sh
+++ b/pkgs/build-support/kernel/modules-closure.sh
@@ -19,36 +19,55 @@ version=$(cd $kernel/lib/modules && ls -d *)
 echo "kernel version is $version"
 
 # Determine the dependencies of each root module.
-closure=
+mkdir -p $out/lib/modules/"$version"
+touch closure
 for module in $rootModules; do
     echo "root module: $module"
-    deps=$(modprobe --config no-config -d $kernel --set-version "$version" --show-depends "$module" \
-        | sed 's/^insmod //') \
-        || if test -z "$allowMissing"; then exit 1; fi
-    if [[ "$deps" != builtin* ]]; then
-        closure="$closure $deps"
+    modprobe --config no-config -d $kernel --set-version "$version" --show-depends "$module" \
+    | while read cmd module args; do
+        case "$cmd" in
+            builtin)
+                touch found
+                echo "$module" >>closure
+                echo "  builtin dependency: $module";;
+            insmod)
+                touch found
+                if ! test -e "$module"; then
+                    echo "  dependency not found: $module"
+                    exit 1
+                fi
+                target=$(echo "$module" | sed "s^$NIX_STORE.*/lib/modules/^$out/lib/modules/^")
+                if test -e "$target"; then
+                    echo "  dependency already copied: $module"
+                    continue
+                fi
+                echo "$module" >>closure
+                echo "  copying dependency: $module"
+                mkdir -p $(dirname $target)
+                cp "$module" "$target"
+                # If the kernel is compiled with coverage instrumentation, it
+                # contains the paths of the *.gcda coverage data output files
+                # (which it doesn't actually use...).  Get rid of them to prevent
+                # the whole kernel from being included in the initrd.
+                nuke-refs "$target"
+                echo "$target" >> $out/insmod-list;;
+             *)
+                echo "  unexpected modprobe output: $cmd $module"
+                exit 1;;
+        esac
+    done || test -n "$allowMissing"
+    if ! test -e found; then
+        echo "  not found"
+        if test -z "$allowMissing"; then
+            exit 1
+        fi
+    else
+        rm found
     fi
 done
 
-echo "closure:"
-mkdir -p $out/lib/modules/"$version"
-for module in $closure; do
-    target=$(echo $module | sed "s^$NIX_STORE.*/lib/modules/^$out/lib/modules/^")
-    if test -e "$target"; then continue; fi
-    if test \! -e "$module"; then continue; fi # XXX: to avoid error with "cp builtin builtin"
-    mkdir -p $(dirname $target)
-    echo $module
-    cp $module $target
-    # If the kernel is compiled with coverage instrumentation, it
-    # contains the paths of the *.gcda coverage data output files
-    # (which it doesn't actually use...).  Get rid of them to prevent
-    # the whole kernel from being included in the initrd.
-    nuke-refs $target
-    echo $target >> $out/insmod-list
-done
-
 mkdir -p $out/lib/firmware
-for module in $closure; do
+for module in $(cat closure); do
     for i in $(modinfo -F firmware $module); do
         mkdir -p "$out/lib/firmware/$(dirname "$i")"
         echo "firmware for $module: $i"

From d32743abe03ed94bcb6dc488c0f982f8645a41cf Mon Sep 17 00:00:00 2001
From: syberant <sybrand@neuralcoding.com>
Date: Fri, 31 Jul 2020 18:26:07 +0200
Subject: [PATCH 02/55] openjump: 1.3.1 -> 1.15 Also fixes #38452

---
 pkgs/applications/misc/openjump/default.nix | 36 ++++++++++-----------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/pkgs/applications/misc/openjump/default.nix b/pkgs/applications/misc/openjump/default.nix
index e537180686cd..544329ec5e79 100644
--- a/pkgs/applications/misc/openjump/default.nix
+++ b/pkgs/applications/misc/openjump/default.nix
@@ -1,33 +1,33 @@
-{ stdenv, fetchurl, unzip, runtimeShell }:
+{ stdenv, fetchurl, unzip, makeWrapper
+, coreutils, gawk, which, gnugrep, findutils
+, jdk
+}:
 
 stdenv.mkDerivation {
-  name = "openjump-1.3.1";
+  pname = "openjump";
+  version = "1.15";
 
   src = fetchurl {
-    url = "mirror://sourceforge/jump-pilot/OpenJUMP/1.3.1/openjump-1.3.1.zip";
-    sha256 = "0y4z53yx0x7rp3c8rnj028ni3gr47r35apgcpqp3jl7r2di6zgqm";
+    url = "mirror://sourceforge/jump-pilot/OpenJUMP/1.15/OpenJUMP-Portable-1.15-r6241-CORE.zip";
+    sha256 = "12snzkv83w6khcdqzp6xahqapwp82af6c7j2q8n0lj62hk79rfgl";
   };
 
-  # ln jump.log hack: a different user will probably get a permission denied
-  # error. Still this is better than getting it always.
-  # TODO: build from source and patch this
+  # TODO: build from source
   unpackPhase = ''
     mkdir -p $out/bin;
     cd $out; unzip $src
-    s=$out/bin/OpenJump
-    dir=$(echo $out/openjump-*)
-    cat >> $s << EOF
-    #!${runtimeShell}
-    cd $dir/bin
-    exec ${stdenv.shell} openjump.sh
-    EOF
-    chmod +x $s
-    ln -s /tmp/openjump.log $dir/bin/jump.log
   '';
 
-  installPhase = ":";
+  buildInputs = [unzip makeWrapper];
 
-  buildInputs = [unzip];
+  installPhase = ''
+    dir=$(echo $out/OpenJUMP-*)
+
+    chmod +x $dir/bin/oj_linux.sh
+    makeWrapper $dir/bin/oj_linux.sh $out/bin/OpenJump \
+      --set JAVA_HOME ${jdk.home} \
+      --set PATH "${coreutils}/bin:${gawk}/bin:${which}/bin:${gnugrep}/bin:${findutils}/bin"
+  '';
 
   meta = {
     description = "Open source Geographic Information System (GIS) written in the Java programming language";

From 447c94f40c9820ca2eff28fd3cc415660732dfd2 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Mon, 10 Aug 2020 01:20:31 +0000
Subject: [PATCH 03/55] asls: 0.4.0 -> 0.4.2

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

diff --git a/pkgs/development/tools/misc/asls/default.nix b/pkgs/development/tools/misc/asls/default.nix
index 8a457593d52f..6999eb3e47a4 100644
--- a/pkgs/development/tools/misc/asls/default.nix
+++ b/pkgs/development/tools/misc/asls/default.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   pname = "asls";
-  version = "0.4.0";
+  version = "0.4.2";
 
   src = fetchurl {
     url = "https://github.com/saulecabrera/asls/releases/download/v${version}/bin.tar.gz";
-    sha256 = "0zy89fvdhk2bj41fzx349gi8237ww96s21hlg6blqmfhvfxsnszg";
+    sha256 = "14dcms0xl6dncwf16vixvf7rq7g15iwq8h4vja0dsiisyfm08aks";
   };
 
   buildInputs = [ erlangR22 ];

From 0418df84f88d452eaaa378ed38cc62cf2ba5baf1 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Mon, 10 Aug 2020 06:49:42 +0000
Subject: [PATCH 04/55] ergo: 3.2.7 -> 3.3.0

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

diff --git a/pkgs/applications/blockchains/ergo/default.nix b/pkgs/applications/blockchains/ergo/default.nix
index e7a83d7496b6..cfd72db7f464 100644
--- a/pkgs/applications/blockchains/ergo/default.nix
+++ b/pkgs/applications/blockchains/ergo/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "ergo";
-  version = "3.2.7";
+  version = "3.3.0";
 
   src = fetchurl {
     url = "https://github.com/ergoplatform/ergo/releases/download/v${version}/ergo-${version}.jar";
-    sha256 = "1ng2q9yp03j8p2xh7rlqad5h4p82ks1l00401pq7m0y02q90szr8";
+    sha256 = "1lja4ba6bm1jk0lh2ra5v8i5g3f1gy7mk2b3yrx1w7x02ll9gr06";
   };
 
   nativeBuildInputs = [ makeWrapper ];

From eeea325e64ad61cf7d1f00051c622298fef93237 Mon Sep 17 00:00:00 2001
From: Henry <cryptix@riseup.net>
Date: Mon, 10 Aug 2020 11:15:01 +0200
Subject: [PATCH 05/55] aliza: 1.48.10 -> 1.98.32

---
 pkgs/applications/science/medicine/aliza/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/medicine/aliza/default.nix b/pkgs/applications/science/medicine/aliza/default.nix
index 279f602e3fd5..b4e56591f9c8 100644
--- a/pkgs/applications/science/medicine/aliza/default.nix
+++ b/pkgs/applications/science/medicine/aliza/default.nix
@@ -3,11 +3,11 @@
 with stdenv.lib;
 stdenv.mkDerivation {
   pname = "aliza";
-  version = "1.48.10";
+  version = "1.98.32";
   src = fetchurl {
     # See https://www.aliza-dicom-viewer.com/download
-    url = "https://drive.google.com/uc?export=download&id=16WEScARaSrzJpJkyGuOUxDF95eUwGyET";
-    sha256 = "1ls16cwd0fmb5axxmy9lgf8cqrf7g7swm26f0gr2vqp4z9bw6qn3";
+    url = "https://drive.google.com/uc?export=download&id=1nggavPhY_633T-AW9PdkcAgbWtzv3QKG";
+    sha256 = "00vbgv8ca9ckgkicyyngrb01yhhcqc8hygg2bls7b44c47hcc8zz";
     name = "aliza.rpm";
   };
 

From 5e8076a1f967888d80968d15d4e086cc1f738dfa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dani=C3=ABl=20de=20Kok?= <me@danieldk.eu>
Date: Mon, 10 Aug 2020 17:07:08 +0200
Subject: [PATCH 06/55] git-quick-stats: properly wrap

git-quick-stats was not properly wrapped, making it fail in pure
and sandboxed environments.
---
 .../tools/git-quick-stats/default.nix         | 36 +++++++++++++++++--
 1 file changed, 34 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/tools/git-quick-stats/default.nix b/pkgs/development/tools/git-quick-stats/default.nix
index 795c8b94cc4b..0ceb6f566a31 100644
--- a/pkgs/development/tools/git-quick-stats/default.nix
+++ b/pkgs/development/tools/git-quick-stats/default.nix
@@ -1,14 +1,46 @@
-{ stdenv, fetchFromGitHub }:
+{ stdenv
+, fetchFromGitHub
+, makeWrapper
+, coreutils
+, gawk
+, git
+, gnugrep
+, ncurses
+, utillinux
+}:
+
 stdenv.mkDerivation rec {
   pname = "git-quick-stats";
   version = "2.1.4";
+
   src = fetchFromGitHub {
     repo = "git-quick-stats";
     owner = "arzzen";
     rev = version;
     sha256 = "0fg0fijghcz7hvbc9y8dfksz0qmsz700kc2mfb03y90kja99v68y";
   };
-  PREFIX = builtins.placeholder "out";
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  installFlags = [
+    "PREFIX=${builtins.placeholder "out"}"
+  ];
+
+  postInstall =
+    let
+      path = stdenv.lib.makeBinPath [
+        coreutils
+        gawk
+        git
+        gnugrep
+        ncurses
+        utillinux
+      ];
+    in
+    ''
+      wrapProgram $out/bin/git-quick-stats --suffix PATH : ${path}
+    '';
+
   meta = with stdenv.lib; {
     homepage = "https://github.com/arzzen/git-quick-stats";
     description = "A simple and efficient way to access various statistics in git repository";

From b5a6cfe4e2a15db9036e3627083670d2e7f14e07 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dani=C3=ABl=20de=20Kok?= <me@danieldk.eu>
Date: Tue, 11 Aug 2020 13:29:02 +0200
Subject: [PATCH 07/55] intel-compute-runtime: add libstdc++ to RPATH

---
 pkgs/os-specific/linux/intel-compute-runtime/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/os-specific/linux/intel-compute-runtime/default.nix b/pkgs/os-specific/linux/intel-compute-runtime/default.nix
index 869041256b62..5a3a5bf7a4d3 100644
--- a/pkgs/os-specific/linux/intel-compute-runtime/default.nix
+++ b/pkgs/os-specific/linux/intel-compute-runtime/default.nix
@@ -43,7 +43,7 @@ stdenv.mkDerivation rec {
   '';
 
   postFixup = ''
-    patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ intel-gmmlib intel-graphics-compiler libva ]} \
+    patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ intel-gmmlib intel-graphics-compiler libva stdenv.cc.cc.lib ]} \
       $out/lib/intel-opencl/libigdrcl.so
   '';
 

From 9b56677634938860eedd06f9415432add0491ad7 Mon Sep 17 00:00:00 2001
From: Aaron Andersen <aaron@fosslib.net>
Date: Tue, 11 Aug 2020 21:09:41 -0400
Subject: [PATCH 08/55] nixos/mysql: remove variable with confusing name

---
 nixos/modules/services/databases/mysql.nix | 26 ++++++++++------------
 1 file changed, 12 insertions(+), 14 deletions(-)

diff --git a/nixos/modules/services/databases/mysql.nix b/nixos/modules/services/databases/mysql.nix
index 2e8c5b7640b2..63e769e0b0bc 100644
--- a/nixos/modules/services/databases/mysql.nix
+++ b/nixos/modules/services/databases/mysql.nix
@@ -6,12 +6,10 @@ let
 
   cfg = config.services.mysql;
 
-  mysql = cfg.package;
-
-  isMariaDB = lib.getName mysql == lib.getName pkgs.mariadb;
+  isMariaDB = lib.getName cfg.package == lib.getName pkgs.mariadb;
 
   mysqldOptions =
-    "--user=${cfg.user} --datadir=${cfg.dataDir} --basedir=${mysql}";
+    "--user=${cfg.user} --datadir=${cfg.dataDir} --basedir=${cfg.package}";
 
   settingsFile = pkgs.writeText "my.cnf" (
     generators.toINI { listsAsDuplicateKeys = true; } cfg.settings +
@@ -329,7 +327,7 @@ in
 
     users.groups.mysql.gid = config.ids.gids.mysql;
 
-    environment.systemPackages = [mysql];
+    environment.systemPackages = [ cfg.package ];
 
     environment.etc."my.cnf".source = cfg.configFile;
 
@@ -357,12 +355,12 @@ in
 
         preStart = if isMariaDB then ''
           if ! test -e ${cfg.dataDir}/mysql; then
-            ${mysql}/bin/mysql_install_db --defaults-file=/etc/my.cnf ${mysqldOptions}
+            ${cfg.package}/bin/mysql_install_db --defaults-file=/etc/my.cnf ${mysqldOptions}
             touch ${cfg.dataDir}/mysql_init
           fi
         '' else ''
           if ! test -e ${cfg.dataDir}/mysql; then
-            ${mysql}/bin/mysqld --defaults-file=/etc/my.cnf ${mysqldOptions} --initialize-insecure
+            ${cfg.package}/bin/mysqld --defaults-file=/etc/my.cnf ${mysqldOptions} --initialize-insecure
             touch ${cfg.dataDir}/mysql_init
           fi
         '';
@@ -372,7 +370,7 @@ in
           Restart = "on-abort";
           RestartSec = "5s";
           # The last two environment variables are used for starting Galera clusters
-          ExecStart = "${mysql}/bin/mysqld --defaults-file=/etc/my.cnf ${mysqldOptions} $_WSREP_NEW_CLUSTER $_WSREP_START_POSITION";
+          ExecStart = "${cfg.package}/bin/mysqld --defaults-file=/etc/my.cnf ${mysqldOptions} $_WSREP_NEW_CLUSTER $_WSREP_START_POSITION";
           ExecStartPost =
             let
               setupScript = pkgs.writeScript "mysql-setup" ''
@@ -416,7 +414,7 @@ in
                                 cat ${database.schema}/mysql-databases/*.sql
                             fi
                             ''}
-                          ) | ${mysql}/bin/mysql -u root -N
+                          ) | ${cfg.package}/bin/mysql -u root -N
                       fi
                     '') cfg.initialDatabases}
 
@@ -428,7 +426,7 @@ in
                           echo "CREATE USER '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}' IDENTIFIED WITH mysql_native_password;"
                           echo "SET PASSWORD FOR '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}' = PASSWORD('${cfg.replication.masterPassword}');"
                           echo "GRANT REPLICATION SLAVE ON *.* TO '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}';"
-                        ) | ${mysql}/bin/mysql -u root -N
+                        ) | ${cfg.package}/bin/mysql -u root -N
                       ''}
 
                     ${optionalString (cfg.replication.role == "slave")
@@ -438,7 +436,7 @@ in
                         ( echo "stop slave;"
                           echo "change master to master_host='${cfg.replication.masterHost}', master_user='${cfg.replication.masterUser}', master_password='${cfg.replication.masterPassword}';"
                           echo "start slave;"
-                        ) | ${mysql}/bin/mysql -u root -N
+                        ) | ${cfg.package}/bin/mysql -u root -N
                       ''}
 
                     ${optionalString (cfg.initialScript != null)
@@ -446,7 +444,7 @@ in
                         # Execute initial script
                         # using toString to avoid copying the file to nix store if given as path instead of string,
                         # as it might contain credentials
-                        cat ${toString cfg.initialScript} | ${mysql}/bin/mysql -u root -N
+                        cat ${toString cfg.initialScript} | ${cfg.package}/bin/mysql -u root -N
                       ''}
 
                     rm ${cfg.dataDir}/mysql_init
@@ -457,7 +455,7 @@ in
                   ${concatMapStrings (database: ''
                     echo "CREATE DATABASE IF NOT EXISTS \`${database}\`;"
                   '') cfg.ensureDatabases}
-                  ) | ${mysql}/bin/mysql -u root -N
+                  ) | ${cfg.package}/bin/mysql -u root -N
                 ''}
 
                 ${concatMapStrings (user:
@@ -466,7 +464,7 @@ in
                       ${concatStringsSep "\n" (mapAttrsToList (database: permission: ''
                         echo "GRANT ${permission} ON ${database} TO '${user.name}'@'localhost';"
                       '') user.ensurePermissions)}
-                    ) | ${mysql}/bin/mysql -u root -N
+                    ) | ${cfg.package}/bin/mysql -u root -N
                   '') cfg.ensureUsers}
               '';
             in

From 85d08220d5a3042ee4917feb9c84822f810142e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Niklas=20Hamb=C3=BCchen?= <mail@nh2.me>
Date: Thu, 30 Jul 2020 03:52:00 +0200
Subject: [PATCH 09/55] mesa: Fix `-Werror=int-conversion` build error on musl.

Upstream PR I made: https://gitlab.freedesktop.org/mesa/mesa/-/merge_requests/6121
---
 pkgs/development/libraries/mesa/default.nix | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/libraries/mesa/default.nix b/pkgs/development/libraries/mesa/default.nix
index 9a2eda5e7104..ee0094b263ce 100644
--- a/pkgs/development/libraries/mesa/default.nix
+++ b/pkgs/development/libraries/mesa/default.nix
@@ -60,7 +60,21 @@ stdenv.mkDerivation {
     ./opencl-install-dir.patch
     ./disk_cache-include-dri-driver-path-in-cache-key.patch
     ./link-radv-with-ld_args_build_id.patch
-  ] # do not prefix user provided dri-drivers-path
+  ]
+    ++ lib.optionals stdenv.hostPlatform.isMusl [
+      # Fix `-Werror=int-conversion` pthread warnings on musl.
+      # TODO: Remove when https://gitlab.freedesktop.org/mesa/mesa/-/merge_requests/6121 is merged and available
+      (fetchpatch {
+        name = "nine_debug-Make-tid-more-type-correct";
+        # Patch adjusted for version `20.1`, before the big mesa dirs change
+        # `gallium: rename 'state tracker' to 'frontend'`.
+        # Patch for versions after that change is at
+        #     https://gitlab.freedesktop.org/mesa/mesa/commit/aebbf819df6d1e3b4745ef16d0e833300ad67044.patch
+        url = "https://gitlab.freedesktop.org/nh2/mesa/commit/3385c49684375f1153a52ed7ccda3f5135268a41.patch";
+        sha256 = "1ci694sqjll44c9g2md4krhk6qlvq51r7ad5rnnfdnf3l8ys0i50";
+      })
+    ]
+    # do not prefix user provided dri-drivers-path
     ++ lib.optional (lib.versionOlder version "19.0.0") (fetchpatch {
       url = "https://gitlab.freedesktop.org/mesa/mesa/commit/f6556ec7d126b31da37c08d7cb657250505e01a0.patch";
       sha256 = "0z6phi8hbrbb32kkp1js7ggzviq7faz1ria36wi4jbc4in2392d9";

From 3792fef4ec8ec089ae244a35172e540d34a9b06c Mon Sep 17 00:00:00 2001
From: Aaron Andersen <aaron@fosslib.net>
Date: Tue, 11 Aug 2020 21:12:59 -0400
Subject: [PATCH 10/55] nixos/mysql: add group option

---
 nixos/modules/services/databases/mysql.nix | 26 +++++++++++++++-------
 1 file changed, 18 insertions(+), 8 deletions(-)

diff --git a/nixos/modules/services/databases/mysql.nix b/nixos/modules/services/databases/mysql.nix
index 63e769e0b0bc..021a9bbe6eb5 100644
--- a/nixos/modules/services/databases/mysql.nix
+++ b/nixos/modules/services/databases/mysql.nix
@@ -59,6 +59,12 @@ in
         description = "User account under which MySQL runs";
       };
 
+      group = mkOption {
+        type = types.str;
+        default = "mysql";
+        description = "Group under which MySQL runs.";
+      };
+
       dataDir = mkOption {
         type = types.path;
         example = "/var/lib/mysql";
@@ -319,21 +325,25 @@ in
       })
     ];
 
-    users.users.mysql = {
-      description = "MySQL server user";
-      group = "mysql";
-      uid = config.ids.uids.mysql;
+    users.users = optionalAttrs (cfg.user == "mysql") {
+      mysql = {
+        description = "MySQL server user";
+        group = cfg.group;
+        uid = config.ids.uids.mysql;
+      };
     };
 
-    users.groups.mysql.gid = config.ids.gids.mysql;
+    users.groups = optionalAttrs (cfg.group == "mysql") {
+      mysql.gid = config.ids.gids.mysql;
+    };
 
     environment.systemPackages = [ cfg.package ];
 
     environment.etc."my.cnf".source = cfg.configFile;
 
     systemd.tmpfiles.rules = [
-      "d '${cfg.dataDir}' 0700 ${cfg.user} mysql - -"
-      "z '${cfg.dataDir}' 0700 ${cfg.user} mysql - -"
+      "d '${cfg.dataDir}' 0700 '${cfg.user}' '${cfg.group}' - -"
+      "z '${cfg.dataDir}' 0700 '${cfg.user}' '${cfg.group}' - -"
     ];
 
     systemd.services.mysql = let
@@ -473,7 +483,7 @@ in
               "+${setupScript}";
           # User and group
           User = cfg.user;
-          Group = "mysql";
+          Group = cfg.group;
           # Runtime directory and mode
           RuntimeDirectory = "mysqld";
           RuntimeDirectoryMode = "0755";

From ff9921f0fd26432b9a7ef46a70eab237fb4865ae Mon Sep 17 00:00:00 2001
From: Aaron Andersen <aaron@fosslib.net>
Date: Tue, 11 Aug 2020 21:15:02 -0400
Subject: [PATCH 11/55] nixos/mysql: loosen mariadb check

---
 nixos/modules/services/databases/mysql.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nixos/modules/services/databases/mysql.nix b/nixos/modules/services/databases/mysql.nix
index 021a9bbe6eb5..c6d30b3796f5 100644
--- a/nixos/modules/services/databases/mysql.nix
+++ b/nixos/modules/services/databases/mysql.nix
@@ -347,7 +347,7 @@ in
     ];
 
     systemd.services.mysql = let
-      hasNotify = (cfg.package == pkgs.mariadb);
+      hasNotify = isMariaDB;
     in {
         description = "MySQL Server";
 

From 31098a03a21b29204c4616d756878e05d399a3da Mon Sep 17 00:00:00 2001
From: Aaron Andersen <aaron@fosslib.net>
Date: Tue, 11 Aug 2020 21:17:02 -0400
Subject: [PATCH 12/55] nixos/mysql: cleanup some descriptions

---
 nixos/modules/services/databases/mysql.nix | 24 +++++++++++-----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/nixos/modules/services/databases/mysql.nix b/nixos/modules/services/databases/mysql.nix
index c6d30b3796f5..4f5d442db8bf 100644
--- a/nixos/modules/services/databases/mysql.nix
+++ b/nixos/modules/services/databases/mysql.nix
@@ -20,7 +20,7 @@ in
 
 {
   imports = [
-    (mkRemovedOptionModule [ "services" "mysql" "pidDir" ] "Don't wait for pidfiles, describe dependencies through systemd")
+    (mkRemovedOptionModule [ "services" "mysql" "pidDir" ] "Don't wait for pidfiles, describe dependencies through systemd.")
     (mkRemovedOptionModule [ "services" "mysql" "rootPassword" ] "Use socket authentication or set the password outside of the nix store.")
   ];
 
@@ -44,19 +44,19 @@ in
         type = types.nullOr types.str;
         default = null;
         example = literalExample "0.0.0.0";
-        description = "Address to bind to. The default is to bind to all addresses";
+        description = "Address to bind to. The default is to bind to all addresses.";
       };
 
       port = mkOption {
         type = types.int;
         default = 3306;
-        description = "Port of MySQL";
+        description = "Port of MySQL.";
       };
 
       user = mkOption {
         type = types.str;
         default = "mysql";
-        description = "User account under which MySQL runs";
+        description = "User account under which MySQL runs.";
       };
 
       group = mkOption {
@@ -68,7 +68,7 @@ in
       dataDir = mkOption {
         type = types.path;
         example = "/var/lib/mysql";
-        description = "Location where MySQL stores its table files";
+        description = "Location where MySQL stores its table files.";
       };
 
       configFile = mkOption {
@@ -175,7 +175,7 @@ in
       initialScript = mkOption {
         type = types.nullOr types.path;
         default = null;
-        description = "A file containing SQL statements to be executed on the first startup. Can be used for granting certain permissions on the database";
+        description = "A file containing SQL statements to be executed on the first startup. Can be used for granting certain permissions on the database.";
       };
 
       ensureDatabases = mkOption {
@@ -263,33 +263,33 @@ in
         serverId = mkOption {
           type = types.int;
           default = 1;
-          description = "Id of the MySQL server instance. This number must be unique for each instance";
+          description = "Id of the MySQL server instance. This number must be unique for each instance.";
         };
 
         masterHost = mkOption {
           type = types.str;
-          description = "Hostname of the MySQL master server";
+          description = "Hostname of the MySQL master server.";
         };
 
         slaveHost = mkOption {
           type = types.str;
-          description = "Hostname of the MySQL slave server";
+          description = "Hostname of the MySQL slave server.";
         };
 
         masterUser = mkOption {
           type = types.str;
-          description = "Username of the MySQL replication user";
+          description = "Username of the MySQL replication user.";
         };
 
         masterPassword = mkOption {
           type = types.str;
-          description = "Password of the MySQL replication user";
+          description = "Password of the MySQL replication user.";
         };
 
         masterPort = mkOption {
           type = types.int;
           default = 3306;
-          description = "Port number on which the MySQL master server runs";
+          description = "Port number on which the MySQL master server runs.";
         };
       };
     };

From e3c210dfd19f60587a98c055266570d0f950edec Mon Sep 17 00:00:00 2001
From: Aaron Andersen <aaron@fosslib.net>
Date: Tue, 11 Aug 2020 21:54:51 -0400
Subject: [PATCH 13/55] nixos/mysql: run ExecStartPost as an unprivileged user

---
 nixos/modules/services/databases/mysql.nix | 26 +++++++++++++---------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/nixos/modules/services/databases/mysql.nix b/nixos/modules/services/databases/mysql.nix
index 4f5d442db8bf..c1a6b895bdd1 100644
--- a/nixos/modules/services/databases/mysql.nix
+++ b/nixos/modules/services/databases/mysql.nix
@@ -321,7 +321,7 @@ in
         binlog-ignore-db = [ "information_schema" "performance_schema" "mysql" ];
       })
       (mkIf (!isMariaDB) {
-        plugin-load-add = optional (cfg.ensureUsers != []) "auth_socket.so";
+        plugin-load-add = "auth_socket.so";
       })
     ];
 
@@ -383,6 +383,8 @@ in
           ExecStart = "${cfg.package}/bin/mysqld --defaults-file=/etc/my.cnf ${mysqldOptions} $_WSREP_NEW_CLUSTER $_WSREP_START_POSITION";
           ExecStartPost =
             let
+              # The super user account to use on *first* run of MySQL server
+              superUser = if isMariaDB then cfg.user else "root";
               setupScript = pkgs.writeScript "mysql-setup" ''
                 #!${pkgs.runtimeShell} -e
 
@@ -405,6 +407,12 @@ in
 
                 if [ -f ${cfg.dataDir}/mysql_init ]
                 then
+                    # While MariaDB comes with a 'mysql' super user account since 10.4.x MySQL does not
+                    # Since we don't want to run this service as 'root' we need to ensure the account exists on first run
+                    ( echo "CREATE USER IF NOT EXISTS '${cfg.user}'@'localhost' IDENTIFIED WITH ${if isMariaDB then "unix_socket" else "auth_socket"};"
+                      echo "GRANT ALL PRIVILEGES ON *.* TO '${cfg.user}'@'localhost' WITH GRANT OPTION;"
+                    ) | ${cfg.package}/bin/mysql -u ${superUser} -N
+
                     ${concatMapStrings (database: ''
                       # Create initial databases
                       if ! test -e "${cfg.dataDir}/${database.name}"; then
@@ -424,7 +432,7 @@ in
                                 cat ${database.schema}/mysql-databases/*.sql
                             fi
                             ''}
-                          ) | ${cfg.package}/bin/mysql -u root -N
+                          ) | ${cfg.package}/bin/mysql -u ${superUser} -N
                       fi
                     '') cfg.initialDatabases}
 
@@ -436,7 +444,7 @@ in
                           echo "CREATE USER '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}' IDENTIFIED WITH mysql_native_password;"
                           echo "SET PASSWORD FOR '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}' = PASSWORD('${cfg.replication.masterPassword}');"
                           echo "GRANT REPLICATION SLAVE ON *.* TO '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}';"
-                        ) | ${cfg.package}/bin/mysql -u root -N
+                        ) | ${cfg.package}/bin/mysql -u ${superUser} -N
                       ''}
 
                     ${optionalString (cfg.replication.role == "slave")
@@ -446,7 +454,7 @@ in
                         ( echo "stop slave;"
                           echo "change master to master_host='${cfg.replication.masterHost}', master_user='${cfg.replication.masterUser}', master_password='${cfg.replication.masterPassword}';"
                           echo "start slave;"
-                        ) | ${cfg.package}/bin/mysql -u root -N
+                        ) | ${cfg.package}/bin/mysql -u ${superUser} -N
                       ''}
 
                     ${optionalString (cfg.initialScript != null)
@@ -454,7 +462,7 @@ in
                         # Execute initial script
                         # using toString to avoid copying the file to nix store if given as path instead of string,
                         # as it might contain credentials
-                        cat ${toString cfg.initialScript} | ${cfg.package}/bin/mysql -u root -N
+                        cat ${toString cfg.initialScript} | ${cfg.package}/bin/mysql -u ${superUser} -N
                       ''}
 
                     rm ${cfg.dataDir}/mysql_init
@@ -465,7 +473,7 @@ in
                   ${concatMapStrings (database: ''
                     echo "CREATE DATABASE IF NOT EXISTS \`${database}\`;"
                   '') cfg.ensureDatabases}
-                  ) | ${cfg.package}/bin/mysql -u root -N
+                  ) | ${cfg.package}/bin/mysql -N
                 ''}
 
                 ${concatMapStrings (user:
@@ -474,13 +482,11 @@ in
                       ${concatStringsSep "\n" (mapAttrsToList (database: permission: ''
                         echo "GRANT ${permission} ON ${database} TO '${user.name}'@'localhost';"
                       '') user.ensurePermissions)}
-                    ) | ${cfg.package}/bin/mysql -u root -N
+                    ) | ${cfg.package}/bin/mysql -N
                   '') cfg.ensureUsers}
               '';
             in
-              # ensureDatbases & ensureUsers depends on this script being run as root
-              # when the user has secured their mysql install
-              "+${setupScript}";
+              "${setupScript}";
           # User and group
           User = cfg.user;
           Group = cfg.group;

From 14245e9ad494a810c4d3f761d794ba13e65cf35d Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Wed, 12 Aug 2020 15:35:56 +0000
Subject: [PATCH 14/55] operator-sdk: 0.19.2 -> 1.0.0

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

diff --git a/pkgs/development/tools/operator-sdk/default.nix b/pkgs/development/tools/operator-sdk/default.nix
index 7e02ada4fe9c..cec885499bff 100644
--- a/pkgs/development/tools/operator-sdk/default.nix
+++ b/pkgs/development/tools/operator-sdk/default.nix
@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "operator-sdk";
-  version = "0.19.2";
+  version = "1.0.0";
 
   src = fetchFromGitHub {
     owner = "operator-framework";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1lmnxw6l6lknvbwmw5xh238i0j452sib37fw8ybxp64zwvj2sac0";
+    sha256 = "1s59rgr0ssics1487mvx0h37zs7dfjimsvkbs2d8wqc3r8asw0g4";
   };
 
-  vendorSha256 = "1xk3zw8w2fynww0z4d66nlclhjf52bk4cv3bh51yyd1mr808lip5";
+  vendorSha256 = "0xvjsiaa3qvlix1fm07z080vh79wg0xyx2s6jqnqn7fb3nh65kn7";
 
   doCheck = false;
 

From ab55fd735a732aee524fd5e2c42c25fd2f35ed66 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Wed, 12 Aug 2020 21:08:57 +0000
Subject: [PATCH 15/55] tendermint: 0.33.6 -> 0.33.8

---
 pkgs/tools/networking/tendermint/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/networking/tendermint/default.nix b/pkgs/tools/networking/tendermint/default.nix
index 4c4013fb36c2..081819458f07 100644
--- a/pkgs/tools/networking/tendermint/default.nix
+++ b/pkgs/tools/networking/tendermint/default.nix
@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "tendermint";
-  version = "0.33.6";
+  version = "0.33.8";
 
   src = fetchFromGitHub {
     owner = "tendermint";
     repo = pname;
     rev = "v${version}";
-    sha256 = "17zy18s9373f3fp6bqjgj02irzasfv3b6axi84kw7da17mq68vnv";
+    sha256 = "1dcr60gmbkb6833n49mjmlr082ahlv7alaqycl8g3d4f93kdm5c3";
   };
 
   vendorSha256 = "0i0n89lal99fqnzva51kp9f7wzqsfmncpshwxhq26kvykp7ji7sw";

From 843dd42b9e58eb68bf3507dc0b37aedf4a0002e6 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 00:17:27 +0000
Subject: [PATCH 16/55] aha: 0.5 -> 0.5.1

---
 pkgs/tools/text/aha/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/text/aha/default.nix b/pkgs/tools/text/aha/default.nix
index a823f37d8d2c..a096fc128233 100644
--- a/pkgs/tools/text/aha/default.nix
+++ b/pkgs/tools/text/aha/default.nix
@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   pname = "aha";
-  version = "0.5";
+  version = "0.5.1";
 
   src = fetchFromGitHub {
-    sha256 = "0byml4rmpiaalwx69jcixl3yvpvwmwiss1jzgsqwshilb2p4qnmz";
+    sha256 = "1gywad0rvvz3c5balz8cxsnx0562hj2ngzqyr8zsy2mb4pn0lpgv";
     rev = version;
     repo = "aha";
     owner = "theZiz";

From ecbad9338c01a11ae8c77dc8bede8d3827363250 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 01:21:51 +0000
Subject: [PATCH 17/55] bftpd: 5.4 -> 5.6

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

diff --git a/pkgs/servers/ftp/bftpd/default.nix b/pkgs/servers/ftp/bftpd/default.nix
index bb35ec075dde..7fa8e2c2ad78 100644
--- a/pkgs/servers/ftp/bftpd/default.nix
+++ b/pkgs/servers/ftp/bftpd/default.nix
@@ -5,11 +5,11 @@ let
 
 in stdenv.mkDerivation rec {
   name = "${pname}-${version}";
-  version = "5.4";
+  version = "5.6";
 
   src = fetchurl {
     url = "mirror://sourceforge/project/${pname}/${pname}/${name}/${name}.tar.gz";
-    sha256 = "19fd9r233wkjk8gdxn6qsjgfijiw67a48xhgbm2kq46bx80yf3pg";
+    sha256 = "18ksld775balh0yx2icj7fya9fvjkfgvwznvccdlmhi3zidg550h";
   };
 
   preConfigure = ''

From c31f704424461f4ed9e7901fb1c011dc4336358c Mon Sep 17 00:00:00 2001
From: Mario Rodas <marsam@users.noreply.github.com>
Date: Thu, 13 Aug 2020 04:20:00 +0000
Subject: [PATCH 18/55] bftpd: enable on darwin

---
 pkgs/servers/ftp/bftpd/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/servers/ftp/bftpd/default.nix b/pkgs/servers/ftp/bftpd/default.nix
index 7fa8e2c2ad78..538877169e1a 100644
--- a/pkgs/servers/ftp/bftpd/default.nix
+++ b/pkgs/servers/ftp/bftpd/default.nix
@@ -31,6 +31,6 @@ in stdenv.mkDerivation rec {
     homepage = "http://bftpd.sf.net/";
     license = licenses.gpl2Plus;
     maintainers = with maintainers; [ raskin ];
-    platforms = platforms.linux;
+    platforms = platforms.all;
   };
 }

From 79ae3e24df09aadffc44eb626a89794842253915 Mon Sep 17 00:00:00 2001
From: Mario Rodas <marsam@users.noreply.github.com>
Date: Thu, 13 Aug 2020 04:20:00 +0000
Subject: [PATCH 19/55] aha: enable on darwin

---
 pkgs/tools/text/aha/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/tools/text/aha/default.nix b/pkgs/tools/text/aha/default.nix
index a096fc128233..1a6d65c52cd8 100644
--- a/pkgs/tools/text/aha/default.nix
+++ b/pkgs/tools/text/aha/default.nix
@@ -23,6 +23,6 @@ stdenv.mkDerivation rec {
     homepage = "https://github.com/theZiz/aha";
     license = with licenses; [ lgpl2Plus mpl11 ];
     maintainers = with maintainers; [ pSub ];
-    platforms = platforms.linux;
+    platforms = platforms.all;
   };
 }

From 82f62b22477f1c2f32d5366f8147b6a8b85f333f Mon Sep 17 00:00:00 2001
From: Mario Rodas <marsam@users.noreply.github.com>
Date: Thu, 13 Aug 2020 04:20:00 +0000
Subject: [PATCH 20/55] vale: 2.3.0 -> 2.3.2

---
 pkgs/tools/text/vale/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/text/vale/default.nix b/pkgs/tools/text/vale/default.nix
index 01e2a366b657..65b2678dfc09 100644
--- a/pkgs/tools/text/vale/default.nix
+++ b/pkgs/tools/text/vale/default.nix
@@ -2,7 +2,7 @@
 
 buildGoModule rec {
   pname = "vale";
-  version = "2.3.0";
+  version = "2.3.2";
 
   subPackages = [ "." ];
   outputs = [ "out" "data" ];
@@ -11,7 +11,7 @@ buildGoModule rec {
     owner  = "errata-ai";
     repo   = "vale";
     rev    = "v${version}";
-    sha256 = "0jxlh8dlhhqw1mrhp42nywnp6wwpk7nw373s89lp3khhqwb1n08f";
+    sha256 = "0accs8ygg2h5hk8n4d5hs1fpxp9mlbzic6f4dwrygi463z7c3icc";
   };
 
   vendorSha256 = null;

From 49d51914b6e49b731c50fbe09472cbd0587ff520 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 04:30:00 +0000
Subject: [PATCH 21/55] btfs: 2.21 -> 2.22

---
 pkgs/os-specific/linux/btfs/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/os-specific/linux/btfs/default.nix b/pkgs/os-specific/linux/btfs/default.nix
index 146a66154241..b4107e8ba001 100644
--- a/pkgs/os-specific/linux/btfs/default.nix
+++ b/pkgs/os-specific/linux/btfs/default.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   pname = "btfs";
-  version = "2.21";
+  version = "2.22";
 
   src = fetchFromGitHub {
     owner  = "johang";
     repo   = pname;
     rev    = "v${version}";
-    sha256 = "0zqkzfc49jl9kn3m0cg7q0156xyzrdl5w4v70p16sqxdly86mwb0";
+    sha256 = "1z88bk1z4sns3jdn56x83mvh06snxg0lr5h4v0c24lzlf5wbdifz";
   };
 
   nativeBuildInputs = [ autoreconfHook pkgconfig ];

From a2992d836c47fbdc2f949f996fcd41ec5cf0c407 Mon Sep 17 00:00:00 2001
From: Johannes Schleifenbaum <johannes@js-webcoding.de>
Date: Sun, 9 Aug 2020 08:15:24 +0200
Subject: [PATCH 22/55] pythonPackages.jellyfin-apiclient-python: 1.5.1 ->
 1.6.1

---
 .../python-modules/jellyfin-apiclient-python/default.nix      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/jellyfin-apiclient-python/default.nix b/pkgs/development/python-modules/jellyfin-apiclient-python/default.nix
index 79a711d07d05..33c14dbaeb2d 100644
--- a/pkgs/development/python-modules/jellyfin-apiclient-python/default.nix
+++ b/pkgs/development/python-modules/jellyfin-apiclient-python/default.nix
@@ -3,14 +3,14 @@
 
 buildPythonPackage rec {
   pname = "jellyfin-apiclient-python";
-  version = "1.5.1";
+  version = "1.6.1";
   disabled = pythonOlder "3.6";
 
   src = fetchFromGitHub {
     owner = "iwalton3";
     repo = "jellyfin-apiclient-python";
     rev = "v${version}";
-    sha256 = "1mzs4i9c4cf7pmymsyzs8x17hvjs8g9wr046l4f85rkzmz23v1rp";
+    sha256 = "0f7czq83ic22fz1vnf0cavb7l3grcxxd5yyw9wcjz3g1j2d76735";
   };
 
   propagatedBuildInputs = [ requests websocket_client ];

From daa7574361bd0b3a4b17cfa618924d16ce562cfa Mon Sep 17 00:00:00 2001
From: Johannes Schleifenbaum <johannes@js-webcoding.de>
Date: Tue, 4 Aug 2020 12:41:13 +0200
Subject: [PATCH 23/55] jellyfin-mpv-shim: 1.5.11 -> 1.7.1

---
 .../video/jellyfin-mpv-shim/default.nix       | 19 +++++++++-----
 .../disable-desktop-client.patch              | 12 +++++++++
 .../disable-update-check.patch                | 15 +++++++++++
 .../video/jellyfin-mpv-shim/shader-pack.nix   | 25 +++++++++++++++++++
 4 files changed, 65 insertions(+), 6 deletions(-)
 create mode 100644 pkgs/applications/video/jellyfin-mpv-shim/disable-desktop-client.patch
 create mode 100644 pkgs/applications/video/jellyfin-mpv-shim/disable-update-check.patch
 create mode 100644 pkgs/applications/video/jellyfin-mpv-shim/shader-pack.nix

diff --git a/pkgs/applications/video/jellyfin-mpv-shim/default.nix b/pkgs/applications/video/jellyfin-mpv-shim/default.nix
index 4021fda68b9a..825aac4dad29 100644
--- a/pkgs/applications/video/jellyfin-mpv-shim/default.nix
+++ b/pkgs/applications/video/jellyfin-mpv-shim/default.nix
@@ -1,19 +1,27 @@
-{ stdenv, buildPythonApplication, fetchFromGitHub, fetchurl
+{ stdenv, buildPythonApplication, fetchFromGitHub, callPackage
 , mpv, python-mpv-jsonipc, jellyfin-apiclient-python
 , pillow, tkinter, pystray, jinja2, pywebview }:
 
+let
+  shaderPack = callPackage ./shader-pack.nix {};
+in
 buildPythonApplication rec {
   pname = "jellyfin-mpv-shim";
-  version = "1.5.11";
+  version = "1.7.1";
 
   src = fetchFromGitHub {
     owner = "iwalton3";
     repo = pname;
     rev = "v${version}";
-    sha256 = "14hm8yccdp7w1vdnvdzafk1byhaq1qsr33i4962s1nvm9lafxkr7";
+    sha256 = "0alrh5h3f8pq9mrq09jmpqa0yslxsjqwij6kwn24ggbwc10zkq75";
     fetchSubmodules = true; # needed for display_mirror css file
   };
 
+  patches = [
+    ./disable-desktop-client.patch
+    ./disable-update-check.patch
+  ];
+
   # override $HOME directory:
   #   error: [Errno 13] Permission denied: '/homeless-shelter'
   #
@@ -25,10 +33,9 @@ buildPythonApplication rec {
     rm jellyfin_mpv_shim/win_utils.py
   '';
 
-  # disable the desktop client for now
   postPatch = ''
-    substituteInPlace setup.py \
-      --replace "'jellyfin-mpv-desktop=jellyfin_mpv_shim.mpv_shim:main_desktop'," ""
+    # link the default shader pack
+    ln -s ${shaderPack} jellyfin_mpv_shim/default_shader_pack
   '';
 
   propagatedBuildInputs = [
diff --git a/pkgs/applications/video/jellyfin-mpv-shim/disable-desktop-client.patch b/pkgs/applications/video/jellyfin-mpv-shim/disable-desktop-client.patch
new file mode 100644
index 000000000000..996225efb3a5
--- /dev/null
+++ b/pkgs/applications/video/jellyfin-mpv-shim/disable-desktop-client.patch
@@ -0,0 +1,12 @@
+diff --git a/setup.py b/setup.py
+index a831959..2206e6e 100644
+--- a/setup.py
++++ b/setup.py
+@@ -25,7 +25,6 @@ setup(
+     entry_points={
+         'console_scripts': [
+             'jellyfin-mpv-shim=jellyfin_mpv_shim.mpv_shim:main',
+-            'jellyfin-mpv-desktop=jellyfin_mpv_shim.mpv_shim:main_desktop',
+         ]
+     },
+     classifiers=[
diff --git a/pkgs/applications/video/jellyfin-mpv-shim/disable-update-check.patch b/pkgs/applications/video/jellyfin-mpv-shim/disable-update-check.patch
new file mode 100644
index 000000000000..6941b956e854
--- /dev/null
+++ b/pkgs/applications/video/jellyfin-mpv-shim/disable-update-check.patch
@@ -0,0 +1,15 @@
+diff --git a/jellyfin_mpv_shim/conf.py b/jellyfin_mpv_shim/conf.py
+index 0ab9326..ccedc17 100644
+--- a/jellyfin_mpv_shim/conf.py
++++ b/jellyfin_mpv_shim/conf.py
+@@ -88,8 +88,8 @@ class Settings(object):
+         "sync_revert_seek":     True,
+         "sync_osd_message":     True,
+         "screenshot_menu":      True,
+-        "check_updates":        True,
+-        "notify_updates":       True,
++        "check_updates":        False,
++        "notify_updates":       False,
+         "lang":                 None,
+         "desktop_scale":        1.0,
+     }
diff --git a/pkgs/applications/video/jellyfin-mpv-shim/shader-pack.nix b/pkgs/applications/video/jellyfin-mpv-shim/shader-pack.nix
new file mode 100644
index 000000000000..fd33e8c90b52
--- /dev/null
+++ b/pkgs/applications/video/jellyfin-mpv-shim/shader-pack.nix
@@ -0,0 +1,25 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "jellyfin-mpv-shim-shader-pack";
+  version = "1.0.0";
+
+  src = fetchFromGitHub {
+    owner = "iwalton3";
+    repo = "default-shader-pack";
+    rev = "v${version}";
+    sha256 = "04y8gvjy4v3773b1kyan4dxqcf86b56x7v33m2k246jbn0rl2pgr";
+  };
+
+  installPhase = ''
+    mkdir -p $out
+    cp -a . $out
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/iwalton3/default-shader-pack";
+    description = "Preconfigured set of MPV shaders and configurations for MPV Shim media clients";
+    license = with licenses; [ mit lgpl3Plus unlicense ];
+    maintainers = with maintainers; [ jojosch ];
+  };
+}

From b08cf3cd4526c08147b8a3c3e0d911324e759cee Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 06:54:09 +0000
Subject: [PATCH 24/55] bpytop: 1.0.0 -> 1.0.13

---
 pkgs/tools/system/bpytop/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/system/bpytop/default.nix b/pkgs/tools/system/bpytop/default.nix
index 015d9d3adacc..2751689209ba 100644
--- a/pkgs/tools/system/bpytop/default.nix
+++ b/pkgs/tools/system/bpytop/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "bpytop";
-  version = "1.0.0";
+  version = "1.0.13";
 
   src = fetchFromGitHub {
     owner = "aristocratos";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0cxyrk5a9j0ymll9h5b6jq48yjy9srcxh4rmsqk8w0d14prmflgg";
+    sha256 = "1mrzl5ry5janifykp58gf5g7xw7522wvpp8hgq2hpfx52z6my1bj";
   };
 
   buildInputs = [ makeWrapper ];

From 9d38a815790fe65e6548707c9ed2450e7b65c0a7 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 07:36:55 +0000
Subject: [PATCH 25/55] chezmoi: 1.8.3 -> 1.8.4

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

diff --git a/pkgs/tools/misc/chezmoi/default.nix b/pkgs/tools/misc/chezmoi/default.nix
index 59e6a174bfa2..ad27d146742a 100644
--- a/pkgs/tools/misc/chezmoi/default.nix
+++ b/pkgs/tools/misc/chezmoi/default.nix
@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "chezmoi";
-  version = "1.8.3";
+  version = "1.8.4";
 
   src = fetchFromGitHub {
     owner = "twpayne";
     repo = "chezmoi";
     rev = "v${version}";
-    sha256 = "01px0nj2llas835g1hf8lvhigip4jm4innjacz18c7nf1ddwn7ss";
+    sha256 = "0m8ik01y1lag3mgg3g4rxvzndh86b972hv2702dqs28l5zy5h3mv";
   };
 
-  vendorSha256 = "1gzg73lrx73rhb9yj6yakv95m8rz1rhjgqjl1a78c8nvaii27a9x";
+  vendorSha256 = "18s60k7y64z12lx9lgj13fl1jh0aiqinwxrsz751d2iqhgdi2jja";
 
   doCheck = false;
 

From 613f10ef709fb061f7660e900bcaa7687801605e Mon Sep 17 00:00:00 2001
From: Mario Rodas <marsam@users.noreply.github.com>
Date: Thu, 13 Aug 2020 04:20:00 -0500
Subject: [PATCH 26/55] ncspot: 0.2.0 -> 0.2.1

https://github.com/hrkfdn/ncspot/releases/tag/v0.2.1
---
 pkgs/applications/audio/ncspot/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/audio/ncspot/default.nix b/pkgs/applications/audio/ncspot/default.nix
index f284dd3dac1a..90dc4e6db330 100644
--- a/pkgs/applications/audio/ncspot/default.nix
+++ b/pkgs/applications/audio/ncspot/default.nix
@@ -14,16 +14,16 @@ let
 in
 rustPlatform.buildRustPackage rec {
   pname = "ncspot";
-  version = "0.2.0";
+  version = "0.2.1";
 
   src = fetchFromGitHub {
     owner = "hrkfdn";
     repo = "ncspot";
     rev = "v${version}";
-    sha256 = "0b2g5bd04zh1hcrhkgd2srx9gl94da4gpy9arjcvrldschjxjza1";
+    sha256 = "1yx0fc24bgh1x6fdwznc1hqvjq0j7i0zvws3bsyijzs7q48jm0z7";
   };
 
-  cargoSha256 = "1gbhvmg7jfmx0b694rdr3s2zs33d4s645gw1lrxvwffif4mg8fy9";
+  cargoSha256 = "0bh2shg80xbs2cw10dabrdxkvhf2csk5h9wmmk5z87q6w25paz1f";
 
   cargoBuildFlags = [ "--no-default-features" "--features" "${lib.concatStringsSep "," features}" ];
 

From 4451f9b68f317de33f3e2f2e0dec7d8cd9ed2990 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Vladim=C3=ADr=20=C4=8Cun=C3=A1t?= <v@cunat.cz>
Date: Thu, 13 Aug 2020 16:47:15 +0200
Subject: [PATCH 27/55] rtlwifi_new: switch fetchFromGitHub to a working repo

Fixes #95324.
---
 pkgs/os-specific/linux/rtlwifi_new/default.nix | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pkgs/os-specific/linux/rtlwifi_new/default.nix b/pkgs/os-specific/linux/rtlwifi_new/default.nix
index 403f0a400107..78e5510ad17e 100644
--- a/pkgs/os-specific/linux/rtlwifi_new/default.nix
+++ b/pkgs/os-specific/linux/rtlwifi_new/default.nix
@@ -7,9 +7,10 @@ let modDestDir = "$out/lib/modules/${kernel.modDirVersion}/kernel/drivers/net/wi
 in stdenv.mkDerivation rec {
   pname = "rtlwifi_new";
   version = "2019-08-21";
+  # When updating see https://github.com/lwfinger/rtl8723be/issues/17#issuecomment-657326751
 
   src = fetchFromGitHub {
-    owner = "lwfinger";
+    owner = "rtlwifi-linux";
     repo = "rtlwifi_new";
     rev = "a108e3de87c2ed30b71c3c4595b79ab7a2f9e348";
     sha256 = "15kjs9i9vvmn1cdzccd5cljf3m45r4ssm65klkj2fdkf3kljj38k";

From 3c6d35a07e6b5bc1a8bd235d2e643f639f61da5d Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 09:24:11 -0700
Subject: [PATCH 28/55] bazel-kazel: 0.0.10 -> 0.0.11 (#95026)

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

diff --git a/pkgs/development/tools/bazel-kazel/default.nix b/pkgs/development/tools/bazel-kazel/default.nix
index ba314844abee..62c5e6c9ef98 100644
--- a/pkgs/development/tools/bazel-kazel/default.nix
+++ b/pkgs/development/tools/bazel-kazel/default.nix
@@ -2,13 +2,13 @@
 
 buildGoModule rec {
   pname = "bazel-kazel";
-  version = "0.0.10";
+  version = "0.0.11";
 
   src = fetchFromGitHub {
     owner = "kubernetes";
     repo = "repo-infra";
     rev = "v${version}";
-    sha256 = "1l3dz77h58v1sr7k8cabq5bbdif5w96zdcapax69cv1frr9jbrcb";
+    sha256 = "0fcm7gjsv70qxnwbgy2sgx7clyhlfnkvdxsjgcrkaf5xds8hpys7";
   };
 
   vendorSha256 = "1pzkjh4n9ai8yqi98bkdhicjdr2l8j3fckl5n90c2gdcwqyxvgkf";

From a52e98a2187ffee16e67afc8564703efecbe751b Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Thu, 13 Aug 2020 09:30:40 -0700
Subject: [PATCH 29/55] python3Packages.pybfd: remove due to prolonged breakage

---
 .../python-modules/pybfd/default.nix          | 29 -------------------
 pkgs/top-level/python-packages.nix            |  2 --
 2 files changed, 31 deletions(-)
 delete mode 100644 pkgs/development/python-modules/pybfd/default.nix

diff --git a/pkgs/development/python-modules/pybfd/default.nix b/pkgs/development/python-modules/pybfd/default.nix
deleted file mode 100644
index d04d7bfb5af7..000000000000
--- a/pkgs/development/python-modules/pybfd/default.nix
+++ /dev/null
@@ -1,29 +0,0 @@
-{ lib, fetchFromGitHub, buildPythonPackage, isPyPy, isPy3k, libbfd, libopcodes }:
-
-buildPythonPackage {
-  pname = "pybfd";
-  version = "-0.1.1.2017-12-31";
-
-  disabled = isPyPy || isPy3k;
-
-  src = fetchFromGitHub {
-    owner = "orivej";
-    repo = "pybfd";
-    rev = "a10ada53f2a79de7f62f209567806ef1e91794c7";
-    sha256 = "0sxzhlqjyvvx1zr3qrkb57z6s3g6k3ksyn65fdm9lvl0k4dv2k9w";
-  };
-
-  LIBBFD_INCLUDE_DIR = "${libbfd.dev}/include";
-  LIBBFD_LIBRARY = "${libbfd}/lib/libbfd.so";
-  LIBOPCODES_INCLUDE_DIR = "${libopcodes.dev}/include";
-  LIBOPCODES_LIBRARY = "${libopcodes}/lib/libopcodes.so";
-
-  meta = {
-    homepage = "https://github.com/Groundworkstech/pybfd";
-    description = "A Python interface to the GNU Binary File Descriptor (BFD) library";
-    license = lib.licenses.gpl2;
-    platforms = lib.platforms.linux;
-    maintainers = with lib.maintainers; [ orivej ];
-    broken = true;
-  };
-}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 08ef76a0246a..fe093c493116 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -5483,8 +5483,6 @@ in {
 
   batchspawner = callPackage ../development/python-modules/batchspawner { };
 
-  pybfd = callPackage ../development/python-modules/pybfd { };
-
   pybigwig = callPackage ../development/python-modules/pybigwig { };
 
   py2bit = callPackage ../development/python-modules/py2bit { };

From 962e15aebcc433ee64873eff0bab2f022a84988f Mon Sep 17 00:00:00 2001
From: Florian Klink <flokli@flokli.de>
Date: Thu, 13 Aug 2020 18:39:07 +0200
Subject: [PATCH 30/55] nixos: remove StandardOutput=syslog,
 StandardError=syslog lines
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Since systemd 243, docs were already steering users towards using
`journal`:

https://github.com/systemd/systemd/commit/eedaf7f322a850c5d9f49346d43420423fc6f593

systemd 246 will go one step further, it shows warnings for these units
during bootup, and will [automatically convert these occurences to
`journal`](https://github.com/systemd/systemd/commit/f3dc6af20f410702beb8e45ddf77e92289fc90c7):

> [    6.955976] systemd[1]: /nix/store/hwyfgbwg804vmr92fxc1vkmqfq2k9s17-unit-display-manager.service/display-manager.service:27: Standard output type syslog is obsolete, automatically updating to journal. Please update│······················
 your unit file, and consider removing the setting altogether.

So there's no point of keeping `syslog` here, and it's probably a better
idea to just not set it, due to:

> This setting defaults to the value set with DefaultStandardOutput= in
> systemd-system.conf(5), which defaults to journal.
---
 nixos/modules/hardware/ckb-next.nix                     | 1 -
 nixos/modules/security/tpm2.nix                         | 1 -
 nixos/modules/services/security/privacyidea.nix         | 1 -
 nixos/modules/services/system/earlyoom.nix              | 1 -
 nixos/modules/services/wayland/cage.nix                 | 2 --
 nixos/modules/services/web-apps/tt-rss.nix              | 2 --
 nixos/modules/services/x11/display-managers/gdm.nix     | 1 -
 nixos/modules/services/x11/display-managers/lightdm.nix | 1 -
 nixos/tests/virtualbox.nix                              | 1 -
 9 files changed, 11 deletions(-)

diff --git a/nixos/modules/hardware/ckb-next.nix b/nixos/modules/hardware/ckb-next.nix
index fe0ca9f26d54..6932be1c54ca 100644
--- a/nixos/modules/hardware/ckb-next.nix
+++ b/nixos/modules/hardware/ckb-next.nix
@@ -43,7 +43,6 @@ in
         serviceConfig = {
           ExecStart = "${cfg.package}/bin/ckb-next-daemon ${optionalString (cfg.gid != null) "--gid=${builtins.toString cfg.gid}"}";
           Restart = "on-failure";
-          StandardOutput = "syslog";
         };
       };
     };
diff --git a/nixos/modules/security/tpm2.nix b/nixos/modules/security/tpm2.nix
index 13804fb82cba..27f9b58c9755 100644
--- a/nixos/modules/security/tpm2.nix
+++ b/nixos/modules/security/tpm2.nix
@@ -170,7 +170,6 @@ in {
           Restart = "always";
           RestartSec = 30;
           BusName = "com.intel.tss2.Tabrmd";
-          StandardOutput = "syslog";
           ExecStart = "${cfg.abrmd.package}/bin/tpm2-abrmd";
           User = "tss";
           Group = "nogroup";
diff --git a/nixos/modules/services/security/privacyidea.nix b/nixos/modules/services/security/privacyidea.nix
index d6abfd0e2718..c2988858e56c 100644
--- a/nixos/modules/services/security/privacyidea.nix
+++ b/nixos/modules/services/security/privacyidea.nix
@@ -234,7 +234,6 @@ in
           ExecStop = "${pkgs.coreutils}/bin/kill -INT $MAINPID";
           NotifyAccess = "main";
           KillSignal = "SIGQUIT";
-          StandardError = "syslog";
         };
       };
 
diff --git a/nixos/modules/services/system/earlyoom.nix b/nixos/modules/services/system/earlyoom.nix
index c6a001d30eeb..e29bdbe264cc 100644
--- a/nixos/modules/services/system/earlyoom.nix
+++ b/nixos/modules/services/system/earlyoom.nix
@@ -106,7 +106,6 @@ in
       path = optional ecfg.enableNotifications pkgs.dbus;
       serviceConfig = {
         StandardOutput = "null";
-        StandardError = "syslog";
         ExecStart = ''
           ${pkgs.earlyoom}/bin/earlyoom \
           -m ${toString ecfg.freeMemThreshold} \
diff --git a/nixos/modules/services/wayland/cage.nix b/nixos/modules/services/wayland/cage.nix
index c59ca9983a6c..50e424fccbfc 100644
--- a/nixos/modules/services/wayland/cage.nix
+++ b/nixos/modules/services/wayland/cage.nix
@@ -73,8 +73,6 @@ in {
         TTYVTDisallocate = "yes";
         # Fail to start if not controlling the virtual terminal.
         StandardInput = "tty-fail";
-        StandardOutput = "syslog";
-        StandardError = "syslog";
         # Set up a full (custom) user session for the user, required by Cage.
         PAMName = "cage";
       };
diff --git a/nixos/modules/services/web-apps/tt-rss.nix b/nixos/modules/services/web-apps/tt-rss.nix
index 2ea9537b93de..6a29f10d1195 100644
--- a/nixos/modules/services/web-apps/tt-rss.nix
+++ b/nixos/modules/services/web-apps/tt-rss.nix
@@ -632,8 +632,6 @@ let
           User = "${cfg.user}";
           Group = "tt_rss";
           ExecStart = "${pkgs.php}/bin/php ${cfg.root}/update.php --daemon --quiet";
-          StandardOutput = "syslog";
-          StandardError = "syslog";
           Restart = "on-failure";
           RestartSec = "60";
           SyslogIdentifier = "tt-rss";
diff --git a/nixos/modules/services/x11/display-managers/gdm.nix b/nixos/modules/services/x11/display-managers/gdm.nix
index 573049ab07af..23ab7f2ae433 100644
--- a/nixos/modules/services/x11/display-managers/gdm.nix
+++ b/nixos/modules/services/x11/display-managers/gdm.nix
@@ -200,7 +200,6 @@ in
       KillMode = "mixed";
       IgnoreSIGPIPE = "no";
       BusName = "org.gnome.DisplayManager";
-      StandardOutput = "syslog";
       StandardError = "inherit";
       ExecReload = "${pkgs.coreutils}/bin/kill -SIGHUP $MAINPID";
       KeyringMode = "shared";
diff --git a/nixos/modules/services/x11/display-managers/lightdm.nix b/nixos/modules/services/x11/display-managers/lightdm.nix
index 3bee21fa822e..143785db0b4f 100644
--- a/nixos/modules/services/x11/display-managers/lightdm.nix
+++ b/nixos/modules/services/x11/display-managers/lightdm.nix
@@ -253,7 +253,6 @@ in
       KeyringMode = "shared";
       KillMode = "mixed";
       StandardError = "inherit";
-      StandardOutput = "syslog";
     };
 
     environment.etc."lightdm/lightdm.conf".source = lightdmConf;
diff --git a/nixos/tests/virtualbox.nix b/nixos/tests/virtualbox.nix
index aec8da6a2af3..af76e6f98442 100644
--- a/nixos/tests/virtualbox.nix
+++ b/nixos/tests/virtualbox.nix
@@ -198,7 +198,6 @@ let
       systemd.services."vboxtestlog-${name}@" = {
         description = "VirtualBox Test Machine Log For ${name}";
         serviceConfig.StandardInput = "socket";
-        serviceConfig.StandardOutput = "syslog";
         serviceConfig.SyslogIdentifier = "GUEST-${name}";
         serviceConfig.ExecStart = "${pkgs.coreutils}/bin/cat";
       };

From 48dfc9fa97d762bce28cc8372a2dd3805d14c633 Mon Sep 17 00:00:00 2001
From: David Rusu <davidrusu.me@gmail.com>
Date: Thu, 13 Aug 2020 12:51:08 -0400
Subject: [PATCH 31/55] castxml: 0.2.0 -> 0.3.4 (#95080)

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

diff --git a/pkgs/development/tools/castxml/default.nix b/pkgs/development/tools/castxml/default.nix
index 1011f95cce7f..0a455b4d7cdf 100644
--- a/pkgs/development/tools/castxml/default.nix
+++ b/pkgs/development/tools/castxml/default.nix
@@ -8,13 +8,13 @@
 stdenv.mkDerivation rec {
 
   pname   = "CastXML";
-  version = "0.2.0";
+  version = "0.3.4";
 
   src = fetchFromGitHub {
     owner  = pname;
     repo   = pname;
     rev    = "v${version}";
-    sha256 = "1qpgr5hyb692h7l5igmq53m6a6vi4d9qp8ks893cflfx9955h3ip";
+    sha256 = "0ypj67xrgj228myp7l1gsjw1ja97q68nmj98dsd33srmiayqraj4";
   };
 
   nativeBuildInputs = [ cmake ] ++ stdenv.lib.optionals withMan [ pythonPackages.sphinx ];

From 00c48082521d6fbf236abf5c80cd3d2abac9d0df Mon Sep 17 00:00:00 2001
From: Spencer Baugh <sbaugh@catern.com>
Date: Thu, 13 Aug 2020 13:16:48 -0400
Subject: [PATCH 32/55] pythonPackages.exchangelib: 1.12.2 -> 3.2.1

Also marks the package as no longer broken.

Obsoletes PR #95313
---
 .../python-modules/exchangelib/default.nix    | 23 +++++++++++--------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/python-modules/exchangelib/default.nix b/pkgs/development/python-modules/exchangelib/default.nix
index ed2a7d69da89..0635f8f027cc 100644
--- a/pkgs/development/python-modules/exchangelib/default.nix
+++ b/pkgs/development/python-modules/exchangelib/default.nix
@@ -1,33 +1,38 @@
 { stdenv, fetchFromGitHub, buildPythonPackage,
-  lxml, tzlocal, python-dateutil, pygments, future, requests-kerberos,
+  pythonOlder,
+  lxml, tzlocal, python-dateutil, pygments, requests-kerberos,
   defusedxml, cached-property, isodate, requests_ntlm, dnspython,
-  psutil, requests-mock, pyyaml
+  psutil, requests-mock, pyyaml,
+  oauthlib, requests_oauthlib,
+  flake8,
 }:
 
 buildPythonPackage rec {
   pname = "exchangelib";
-  version = "1.12.2";
+  version = "3.2.1";
+  disabled = pythonOlder "3.5";
 
   # tests are not present in the PyPI version
   src = fetchFromGitHub {
     owner = "ecederstrand";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1p24fq6f46j0qd0ccb64mncxbnm2n9w0sqpl4zk113caaaxkpjil";
+    sha256 = "1sh780q2iwdm3bnlnfdacracf0n7jhbv0g39cdx65v3d510zp4jv";
   };
 
-  # one test is failing due to it trying to send a request to example.com
-  patches = [ ./skip_failing_test.patch ];
-  checkInputs = [ psutil requests-mock pyyaml ];
+  checkInputs = [ psutil requests-mock pyyaml
+    flake8
+  ];
   propagatedBuildInputs = [
     lxml tzlocal python-dateutil pygments requests-kerberos
-    future defusedxml cached-property isodate requests_ntlm dnspython ];
+    defusedxml cached-property isodate requests_ntlm dnspython
+    oauthlib requests_oauthlib
+  ];
 
   meta = with stdenv.lib; {
     description = "Client for Microsoft Exchange Web Services (EWS)";
     homepage    = "https://github.com/ecederstrand/exchangelib";
     license     = licenses.bsd2;
     maintainers = with maintainers; [ catern ];
-    broken = true;
   };
 }

From 9c14f5d56eb42335ca166a3583345704f63c421e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dani=C3=ABl=20de=20Kok?= <me@danieldk.eu>
Date: Thu, 13 Aug 2020 15:45:03 +0200
Subject: [PATCH 33/55] nixos/manual: add a section about common GPU
 acceleration issues

---
 nixos/doc/manual/configuration/gpu-accel.xml | 59 ++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/nixos/doc/manual/configuration/gpu-accel.xml b/nixos/doc/manual/configuration/gpu-accel.xml
index 0aa629cce98f..dc806e8812d4 100644
--- a/nixos/doc/manual/configuration/gpu-accel.xml
+++ b/nixos/doc/manual/configuration/gpu-accel.xml
@@ -190,4 +190,63 @@ GPU1:
       </para>
     </section>
   </section>
+
+  <section xml:id="sec-gpu-accel-common-issues">
+   <title>Common issues</title>
+
+   <section xml:id="sec-gpu-accel-common-issues-permissions">
+    <title>User permissions</title>
+
+    <para>
+     Except where noted explicitly, it should not be necessary to
+     adjust user permissions to use these acceleration APIs. In the default
+     configuration, GPU devices have world-read/write permissions
+     (<filename>/dev/dri/renderD*</filename>) or are tagged as
+     <code>uaccess</code> (<filename>/dev/dri/card*</filename>).  The
+     access control lists of devices with the <varname>uaccess</varname>
+     tag will be updated automatically when a user logs in through
+     <command>systemd-logind</command>. For example, if the user
+     <emphasis>jane</emphasis> is logged in, the access control list
+     should look as follows:
+
+     <screen><prompt>$</prompt> getfacl /dev/dri/card0
+# file: dev/dri/card0
+# owner: root
+# group: video
+user::rw-
+user:jane:rw-
+group::rw-
+mask::rw-
+other::---</screen>
+
+     If you disabled (this functionality of) <command>systemd-logind</command>,
+     you may need to add the user to the <code>video</code> group and
+     log in again.
+    </para>
+   </section>
+
+   <section xml:id="sec-gpu-accel-common-issues-mixing-nixpkgs">
+    <title>Mixing different versions of nixpkgs</title>
+
+    <para>
+     The <emphasis>Installable Client Driver</emphasis> (ICD)
+     mechanism used by OpenCL and Vulkan loads runtimes into its address
+     space using <code>dlopen</code>. Mixing an ICD loader mechanism and
+     runtimes from different version of nixpkgs may not work. For example,
+     if the ICD loader uses an older version of <package>glibc</package>
+     than the runtime, the runtime may not be loadable due to
+     missing symbols. Unfortunately, the loader will generally be quiet
+     about such issues.
+    </para>
+
+    <para>
+     If you suspect that you are running into library version mismatches
+     between an ICL loader and a runtime, you could run an application with
+     the <code>LD_DEBUG</code> variable set to get more diagnostic
+     information. For example, OpenCL can be tested with
+     <code>LD_DEBUG=files clinfo</code>, which should report missing
+     symbols.
+    </para>
+   </section>
+  </section>
 </chapter>

From 1407bada02847119d7876011b36b8c1d1233dda3 Mon Sep 17 00:00:00 2001
From: Louis Tim Larsen <louis@louis.dk>
Date: Sat, 8 Aug 2020 21:07:51 +0200
Subject: [PATCH 34/55] thunderbird: Enable official branding by default

---
 .../networking/mailreaders/thunderbird/68.nix    | 16 ++++++++++------
 .../mailreaders/thunderbird/default.nix          | 16 ++++++++++------
 2 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/pkgs/applications/networking/mailreaders/thunderbird/68.nix b/pkgs/applications/networking/mailreaders/thunderbird/68.nix
index 4b1efef027e0..f4d455085688 100644
--- a/pkgs/applications/networking/mailreaders/thunderbird/68.nix
+++ b/pkgs/applications/networking/mailreaders/thunderbird/68.nix
@@ -62,12 +62,16 @@
 , waylandSupport ? true
 , libxkbcommon, calendarSupport ? true
 
-, # If you want the resulting program to call itself "Thunderbird" instead
-# of "Earlybird" or whatever, enable this option.  However, those
-# binaries may not be distributed without permission from the
-# Mozilla Foundation, see
-# http://www.mozilla.org/foundation/trademarks/.
-enableOfficialBranding ? false
+# As stated by Sylvestre Ledru (@sylvestre) on Nov 22, 2017 at
+# https://github.com/NixOS/nixpkgs/issues/31843#issuecomment-346372756 we
+# have permission to use the official branding.
+#
+# For purposes of documentation the statement of @sylvestre:
+# > As the person who did part of the work described in the LWN article
+# > and release manager working for Mozilla, I can confirm the statement
+# > that I made in
+# > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=815006
+, enableOfficialBranding ? true
 }:
 
 assert waylandSupport -> gtk3Support == true;
diff --git a/pkgs/applications/networking/mailreaders/thunderbird/default.nix b/pkgs/applications/networking/mailreaders/thunderbird/default.nix
index 961806fa9aba..749e24faff68 100644
--- a/pkgs/applications/networking/mailreaders/thunderbird/default.nix
+++ b/pkgs/applications/networking/mailreaders/thunderbird/default.nix
@@ -60,12 +60,16 @@
 , waylandSupport ? true
 , libxkbcommon, calendarSupport ? true
 
-, # If you want the resulting program to call itself "Thunderbird" instead
-# of "Earlybird" or whatever, enable this option.  However, those
-# binaries may not be distributed without permission from the
-# Mozilla Foundation, see
-# http://www.mozilla.org/foundation/trademarks/.
-enableOfficialBranding ? false
+# As stated by Sylvestre Ledru (@sylvestre) on Nov 22, 2017 at
+# https://github.com/NixOS/nixpkgs/issues/31843#issuecomment-346372756 we
+# have permission to use the official branding.
+#
+# For purposes of documentation the statement of @sylvestre:
+# > As the person who did part of the work described in the LWN article
+# > and release manager working for Mozilla, I can confirm the statement
+# > that I made in
+# > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=815006
+, enableOfficialBranding ? true
 }:
 
 assert waylandSupport -> gtk3Support == true;

From 0dbd3c8d0f77a400f9647e97b01644d4332c36ef Mon Sep 17 00:00:00 2001
From: 0x4A6F <0x4A6F@users.noreply.github.com>
Date: Thu, 13 Aug 2020 17:20:46 +0000
Subject: [PATCH 35/55] timescale-prometheus: init at 0.1.0-beta.1

---
 .../timescale-prometheus/default.nix          | 28 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 30 insertions(+)
 create mode 100644 pkgs/servers/monitoring/timescale-prometheus/default.nix

diff --git a/pkgs/servers/monitoring/timescale-prometheus/default.nix b/pkgs/servers/monitoring/timescale-prometheus/default.nix
new file mode 100644
index 000000000000..7a50fb3b0476
--- /dev/null
+++ b/pkgs/servers/monitoring/timescale-prometheus/default.nix
@@ -0,0 +1,28 @@
+{ stdenv
+, buildGoModule
+, fetchFromGitHub
+}:
+
+buildGoModule rec {
+  pname = "timescale-prometheus";
+  version = "0.1.0-beta.1";
+
+  src = fetchFromGitHub {
+    owner = "timescale";
+    repo = pname;
+    rev = "${version}";
+    sha256 = "1q6xky4h9x4j2f0f6ajxwlnqq1pgd2n0z1ldrcifyamd90qkwcm5";
+  };
+
+  vendorSha256 = "sha256:1vp30y59w8mksqxy9ic37vj1jw4lbq24ahhb08a72rysylw94r57";
+
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "An open-source analytical platform for Prometheus metrics";
+    homepage = "https://github.com/timescale/timescale-prometheus";
+    license = licenses.asl20;
+    platforms = platforms.unix;
+    maintainers = [ maintainers."0x4A6F" ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 79a8951e8ab8..0b8e2990b4e7 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -16534,6 +16534,8 @@ in
     asciidoc = asciidoc-full;
   };
 
+  timescale-prometheus = callPackage ../servers/monitoring/timescale-prometheus { };
+
   timescaledb-parallel-copy = callPackage ../development/tools/database/timescaledb-parallel-copy { };
 
   timescaledb-tune = callPackage ../development/tools/database/timescaledb-tune { };

From f1e713feb169cfafbfe07d8e7321123027a34b7c Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 16:07:27 +0000
Subject: [PATCH 36/55] docopt_cpp: 0.6.2 -> 0.6.3

---
 pkgs/development/libraries/docopt_cpp/default.nix | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/libraries/docopt_cpp/default.nix b/pkgs/development/libraries/docopt_cpp/default.nix
index 5c4e71a4f871..36b791ccc98c 100644
--- a/pkgs/development/libraries/docopt_cpp/default.nix
+++ b/pkgs/development/libraries/docopt_cpp/default.nix
@@ -1,14 +1,14 @@
 { stdenv, fetchFromGitHub, cmake, python }:
 
 stdenv.mkDerivation rec {
-  version = "0.6.2";
+  version = "0.6.3";
   pname = "docopt.cpp";
 
   src = fetchFromGitHub {
     owner = "docopt";
     repo = "docopt.cpp";
     rev = "v${version}";
-    sha256 = "1rgkc8nsc2zz2lkyai0y68vrd6i6kbq63hm3vdza7ab6ghq0n1dd";
+    sha256 = "0cz3vv7g5snfbsqcf3q8bmd6kv5qp84gj3avwkn4vl00krw13bl7";
   };
 
   nativeBuildInputs = [ cmake python ];
@@ -17,6 +17,12 @@ stdenv.mkDerivation rec {
 
   doCheck = true;
 
+  postPatch = ''
+    substituteInPlace docopt.pc.in \
+      --replace "@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@" \
+                "@CMAKE_INSTALL_LIBDIR@"
+  '';
+
   checkPhase = "LD_LIBRARY_PATH=$(pwd) python ./run_tests";
 
   meta = with stdenv.lib; {
@@ -27,4 +33,3 @@ stdenv.mkDerivation rec {
     maintainers = with maintainers; [ knedlsepp ];
   };
 }
-

From 0a4a62459ac97d29e95d751771223e772a6fa4d6 Mon Sep 17 00:00:00 2001
From: Jan Tojnar <jtojnar@gmail.com>
Date: Thu, 13 Aug 2020 20:36:11 +0200
Subject: [PATCH 37/55] nixos/fontconfig: Reintroduce unversioned fonts.conf

Turns out lot of software (including Chromium) use bundled fontconfig
so we either need to wrap every one of those, or re-introduce the global unversioned config.
The latter is easier but weakens hermetic configs. But perhaps those are not really worth the effort.
---
 nixos/modules/config/fonts/fontconfig.nix | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nixos/modules/config/fonts/fontconfig.nix b/nixos/modules/config/fonts/fontconfig.nix
index 12a40fbb5a27..846430194716 100644
--- a/nixos/modules/config/fonts/fontconfig.nix
+++ b/nixos/modules/config/fonts/fontconfig.nix
@@ -182,6 +182,9 @@ let
     # fonts.conf
     ln -s ${pkg.out}/etc/fonts/fonts.conf \
           $dst/../fonts.conf
+    # TODO: remove this legacy symlink once people stop using packages built before #95358 was merged
+    ln -s /etc/fonts/${pkg.configVersion}/fonts.conf \
+          $out/etc/fonts/fonts.conf
 
     # fontconfig default config files
     ln -s ${pkg.out}/etc/fonts/conf.d/*.conf \

From 5f72f7c27f7abcacd626756a995a0d0b45aa793a Mon Sep 17 00:00:00 2001
From: Michael Weiss <dev.primeos@gmail.com>
Date: Thu, 13 Aug 2020 20:54:00 +0200
Subject: [PATCH 38/55] jekyll: Update the dependencies (security,
 CVE-2020-14001)

This fixes a potential security issue (reported by bundler-audit) by
updating kramdown to 2.3.0 for CVE-2020-14001 [0].

[0]: https://github.com/advisories/GHSA-mqm2-cgpr-p4m6
---
 .../misc/jekyll/basic/Gemfile.lock            | 14 ++++----
 .../applications/misc/jekyll/basic/gemset.nix | 28 ++++++++--------
 .../misc/jekyll/full/Gemfile.lock             | 16 +++++-----
 pkgs/applications/misc/jekyll/full/gemset.nix | 32 +++++++++----------
 4 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/pkgs/applications/misc/jekyll/basic/Gemfile.lock b/pkgs/applications/misc/jekyll/basic/Gemfile.lock
index 86f1bf23a6b5..ffc7c0e2aebf 100644
--- a/pkgs/applications/misc/jekyll/basic/Gemfile.lock
+++ b/pkgs/applications/misc/jekyll/basic/Gemfile.lock
@@ -10,7 +10,7 @@ GEM
     addressable (2.7.0)
       public_suffix (>= 2.0.2, < 5.0)
     colorator (1.1.0)
-    concurrent-ruby (1.1.6)
+    concurrent-ruby (1.1.7)
     em-websocket (0.5.1)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
@@ -18,11 +18,11 @@ GEM
     ffi (1.13.1)
     forwardable-extended (2.6.0)
     gemoji (3.0.1)
-    html-pipeline (2.13.0)
+    html-pipeline (2.14.0)
       activesupport (>= 2)
       nokogiri (>= 1.4)
     http_parser.rb (0.6.0)
-    i18n (1.8.3)
+    i18n (1.8.5)
       concurrent-ruby (~> 1.0)
     jekyll (4.1.1)
       addressable (~> 2.4)
@@ -56,7 +56,7 @@ GEM
       gemoji (~> 3.0)
       html-pipeline (~> 2.2)
       jekyll (>= 3.0, < 5.0)
-    kramdown (2.2.1)
+    kramdown (2.3.0)
       rexml
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
@@ -67,7 +67,7 @@ GEM
     mercenary (0.4.0)
     mini_portile2 (2.4.0)
     minitest (5.14.1)
-    nokogiri (1.10.9)
+    nokogiri (1.10.10)
       mini_portile2 (~> 2.4.0)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
@@ -76,7 +76,7 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rexml (3.2.4)
-    rouge (3.20.0)
+    rouge (3.22.0)
     safe_yaml (1.0.5)
     sassc (2.4.0)
       ffi (~> 1.9)
@@ -86,7 +86,7 @@ GEM
     tzinfo (1.2.7)
       thread_safe (~> 0.1)
     unicode-display_width (1.7.0)
-    zeitwerk (2.3.0)
+    zeitwerk (2.4.0)
 
 PLATFORMS
   ruby
diff --git a/pkgs/applications/misc/jekyll/basic/gemset.nix b/pkgs/applications/misc/jekyll/basic/gemset.nix
index e4c8a94fce4b..b14b27f3756b 100644
--- a/pkgs/applications/misc/jekyll/basic/gemset.nix
+++ b/pkgs/applications/misc/jekyll/basic/gemset.nix
@@ -36,10 +36,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "094387x4yasb797mv07cs3g6f08y56virc2rjcpb1k79rzaj3nhl";
+      sha256 = "1vnxrbhi7cq3p4y2v9iwd10v1c7l15is4var14hwnb2jip4fyjzz";
       type = "gem";
     };
-    version = "1.1.6";
+    version = "1.1.7";
   };
   em-websocket = {
     dependencies = ["eventmachine" "http_parser.rb"];
@@ -98,10 +98,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "01snn9z3c2p17d9wfczkdkml6mdffah6fpyzgs9mdskb14m68rq6";
+      sha256 = "080sn9z1a64gv04p318jz10y6lv6qd3avip08rrcmq9k4ihai0f1";
       type = "gem";
     };
-    version = "2.13.0";
+    version = "2.14.0";
   };
   "http_parser.rb" = {
     groups = ["default"];
@@ -119,10 +119,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "10nq1xjqvkhngiygji831qx9bryjwws95r4vrnlq9142bzkg670s";
+      sha256 = "153sx77p16vawrs4qpkv7qlzf9v5fks4g7xqcj1dwk40i6g7rfzk";
       type = "gem";
     };
-    version = "1.8.3";
+    version = "1.8.5";
   };
   jekyll = {
     dependencies = ["addressable" "colorator" "em-websocket" "i18n" "jekyll-sass-converter" "jekyll-watch" "kramdown" "kramdown-parser-gfm" "liquid" "mercenary" "pathutil" "rouge" "safe_yaml" "terminal-table"];
@@ -218,10 +218,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "059mk8lmddp2a2aa6s4pp7x2yyqbqg5crx5jkn32dzlnqi2j5cn6";
+      sha256 = "1vmw752c26ny2jwl0npn0gbyqwgz4hdmlpxnsld9qi9xhk5b1qh7";
       type = "gem";
     };
-    version = "2.2.1";
+    version = "2.3.0";
   };
   kramdown-parser-gfm = {
     dependencies = ["kramdown"];
@@ -291,10 +291,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "12j76d0bp608932xkzmfi638c7aqah57l437q8494znzbj610qnm";
+      sha256 = "0xmf60nj5kg9vaj5bysy308687sgmkasgx06vbbnf94p52ih7si2";
       type = "gem";
     };
-    version = "1.10.9";
+    version = "1.10.10";
   };
   pathutil = {
     dependencies = ["forwardable-extended"];
@@ -353,10 +353,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1r5npy9a95qh5v74lw7ir3nhaq4xrzyhfdixd7c5xy295i92nnic";
+      sha256 = "1wcz7i009wdbymlfsamagqi18m6ih8j60bii0k18f21g70r72i0m";
       type = "gem";
     };
-    version = "3.20.0";
+    version = "3.22.0";
   };
   safe_yaml = {
     groups = ["default"];
@@ -426,9 +426,9 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1akpm3pwvyiack2zk6giv9yn3cqb8pw6g40p4394pdc3xmy3s4k0";
+      sha256 = "0jvn50k76kl14fpymk4hdsf9sk00jl84yxzl783xhnw4dicp0m0k";
       type = "gem";
     };
-    version = "2.3.0";
+    version = "2.4.0";
   };
 }
\ No newline at end of file
diff --git a/pkgs/applications/misc/jekyll/full/Gemfile.lock b/pkgs/applications/misc/jekyll/full/Gemfile.lock
index 9acfaaa97cd1..d79550720658 100644
--- a/pkgs/applications/misc/jekyll/full/Gemfile.lock
+++ b/pkgs/applications/misc/jekyll/full/Gemfile.lock
@@ -17,7 +17,7 @@ GEM
       execjs
     coffee-script-source (1.12.2)
     colorator (1.1.0)
-    concurrent-ruby (1.1.6)
+    concurrent-ruby (1.1.7)
     em-websocket (0.5.1)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
@@ -29,11 +29,11 @@ GEM
     ffi (1.13.1)
     forwardable-extended (2.6.0)
     gemoji (3.0.1)
-    html-pipeline (2.13.0)
+    html-pipeline (2.14.0)
       activesupport (>= 2)
       nokogiri (>= 1.4)
     http_parser.rb (0.6.0)
-    i18n (1.8.3)
+    i18n (1.8.5)
       concurrent-ruby (~> 1.0)
     jekyll (4.1.1)
       addressable (~> 2.4)
@@ -55,7 +55,7 @@ GEM
     jekyll-coffeescript (2.0.0)
       coffee-script (~> 2.2)
       coffee-script-source (~> 1.12)
-    jekyll-feed (0.14.0)
+    jekyll-feed (0.15.0)
       jekyll (>= 3.7, < 5.0)
     jekyll-gist (1.5.0)
       octokit (~> 4.2)
@@ -77,7 +77,7 @@ GEM
       gemoji (~> 3.0)
       html-pipeline (~> 2.2)
       jekyll (>= 3.0, < 5.0)
-    kramdown (2.2.1)
+    kramdown (2.3.0)
       rexml
     kramdown-parser-gfm (1.1.0)
       kramdown (~> 2.0)
@@ -97,7 +97,7 @@ GEM
     mini_portile2 (2.4.0)
     minitest (5.14.1)
     multipart-post (2.1.1)
-    nokogiri (1.10.9)
+    nokogiri (1.10.10)
       mini_portile2 (~> 2.4.0)
     octokit (4.18.0)
       faraday (>= 0.9)
@@ -110,7 +110,7 @@ GEM
       ffi (~> 1.0)
     rdoc (6.2.1)
     rexml (3.2.4)
-    rouge (3.20.0)
+    rouge (3.22.0)
     safe_yaml (1.0.5)
     sassc (2.4.0)
       ffi (~> 1.9)
@@ -125,7 +125,7 @@ GEM
       thread_safe (~> 0.1)
     unicode-display_width (1.7.0)
     yajl-ruby (1.4.1)
-    zeitwerk (2.3.0)
+    zeitwerk (2.4.0)
 
 PLATFORMS
   ruby
diff --git a/pkgs/applications/misc/jekyll/full/gemset.nix b/pkgs/applications/misc/jekyll/full/gemset.nix
index 073f69f5b33b..aa0bc9bcdcc5 100644
--- a/pkgs/applications/misc/jekyll/full/gemset.nix
+++ b/pkgs/applications/misc/jekyll/full/gemset.nix
@@ -90,10 +90,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "094387x4yasb797mv07cs3g6f08y56virc2rjcpb1k79rzaj3nhl";
+      sha256 = "1vnxrbhi7cq3p4y2v9iwd10v1c7l15is4var14hwnb2jip4fyjzz";
       type = "gem";
     };
-    version = "1.1.6";
+    version = "1.1.7";
   };
   em-websocket = {
     dependencies = ["eventmachine" "http_parser.rb"];
@@ -195,10 +195,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "01snn9z3c2p17d9wfczkdkml6mdffah6fpyzgs9mdskb14m68rq6";
+      sha256 = "080sn9z1a64gv04p318jz10y6lv6qd3avip08rrcmq9k4ihai0f1";
       type = "gem";
     };
-    version = "2.13.0";
+    version = "2.14.0";
   };
   "http_parser.rb" = {
     groups = ["default"];
@@ -216,10 +216,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "10nq1xjqvkhngiygji831qx9bryjwws95r4vrnlq9142bzkg670s";
+      sha256 = "153sx77p16vawrs4qpkv7qlzf9v5fks4g7xqcj1dwk40i6g7rfzk";
       type = "gem";
     };
-    version = "1.8.3";
+    version = "1.8.5";
   };
   jekyll = {
     dependencies = ["addressable" "colorator" "em-websocket" "i18n" "jekyll-sass-converter" "jekyll-watch" "kramdown" "kramdown-parser-gfm" "liquid" "mercenary" "pathutil" "rouge" "safe_yaml" "terminal-table"];
@@ -260,10 +260,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0fhbz5wc8cf60dwsbqcr49wygyk5qarpc7g77p6dlwq2r21nil5c";
+      sha256 = "1mgc1ik2cq2g8g7z9ql2i6ydzy771m2i4qrd1q77x8cf2sprlb0z";
       type = "gem";
     };
-    version = "0.14.0";
+    version = "0.15.0";
   };
   jekyll-gist = {
     dependencies = ["octokit"];
@@ -369,10 +369,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "059mk8lmddp2a2aa6s4pp7x2yyqbqg5crx5jkn32dzlnqi2j5cn6";
+      sha256 = "1vmw752c26ny2jwl0npn0gbyqwgz4hdmlpxnsld9qi9xhk5b1qh7";
       type = "gem";
     };
-    version = "2.2.1";
+    version = "2.3.0";
   };
   kramdown-parser-gfm = {
     dependencies = ["kramdown"];
@@ -519,10 +519,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "12j76d0bp608932xkzmfi638c7aqah57l437q8494znzbj610qnm";
+      sha256 = "0xmf60nj5kg9vaj5bysy308687sgmkasgx06vbbnf94p52ih7si2";
       type = "gem";
     };
-    version = "1.10.9";
+    version = "1.10.10";
   };
   octokit = {
     dependencies = ["faraday" "sawyer"];
@@ -602,10 +602,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1r5npy9a95qh5v74lw7ir3nhaq4xrzyhfdixd7c5xy295i92nnic";
+      sha256 = "1wcz7i009wdbymlfsamagqi18m6ih8j60bii0k18f21g70r72i0m";
       type = "gem";
     };
-    version = "3.20.0";
+    version = "3.22.0";
   };
   safe_yaml = {
     groups = ["default"];
@@ -718,9 +718,9 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1akpm3pwvyiack2zk6giv9yn3cqb8pw6g40p4394pdc3xmy3s4k0";
+      sha256 = "0jvn50k76kl14fpymk4hdsf9sk00jl84yxzl783xhnw4dicp0m0k";
       type = "gem";
     };
-    version = "2.3.0";
+    version = "2.4.0";
   };
 }
\ No newline at end of file

From 104cd996e16befa26f1b02163e0cdaa4b4926116 Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Thu, 13 Aug 2020 10:11:58 -0700
Subject: [PATCH 39/55] python3Packages.caldavclientlibrary-asynk: remove due
 to prolonged breakage

---
 .../caldavclientlibrary-asynk/default.nix     | 35 -------------------
 pkgs/top-level/python-packages.nix            |  2 --
 2 files changed, 37 deletions(-)
 delete mode 100644 pkgs/development/python-modules/caldavclientlibrary-asynk/default.nix

diff --git a/pkgs/development/python-modules/caldavclientlibrary-asynk/default.nix b/pkgs/development/python-modules/caldavclientlibrary-asynk/default.nix
deleted file mode 100644
index 2d882967493c..000000000000
--- a/pkgs/development/python-modules/caldavclientlibrary-asynk/default.nix
+++ /dev/null
@@ -1,35 +0,0 @@
-{ stdenv
-, buildPythonPackage
-, fetchgit
-, isPy3k
-}:
-
-buildPythonPackage {
-  version = "asynkdev";
-  pname = "caldavclientlibrary-asynk";
-
-  src = fetchgit {
-    url = "https://github.com/skarra/CalDAVClientLibrary.git";
-    rev = "06699b08190d50cc2636b921a654d67db0a967d1";
-    sha256 = "157q32251ac9x3gdshgrjwsy48nq74vrzviswvph56h9wa8ksnnk";
-  };
-
-  disabled = isPy3k;
-
-  meta = with stdenv.lib; {
-    description = "A Python library and tool for CalDAV";
-
-    longDescription = ''
-      CalDAVCLientLibrary is a Python library and tool for CalDAV.
-
-      This package is the unofficial CalDAVCLientLibrary Python
-      library maintained by the author of Asynk and is needed for
-      that package.
-    '';
-
-    homepage = "https://github.com/skarra/CalDAVClientLibrary/tree/asynkdev/";
-    maintainers = with maintainers; [ pjones ];
-    broken = true; # 2018-04-11
-  };
-
-}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index fe093c493116..4cc74d37bbcc 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -2062,8 +2062,6 @@ in {
 
   caldav = callPackage ../development/python-modules/caldav { };
 
-  caldavclientlibrary-asynk = callPackage ../development/python-modules/caldavclientlibrary-asynk { };
-
   biopython = callPackage ../development/python-modules/biopython { };
 
   bedup = callPackage ../development/python-modules/bedup { };

From 9ccacccc47d38533631c25561d370fe5fd739671 Mon Sep 17 00:00:00 2001
From: Jonathan Ringer <jonringer117@gmail.com>
Date: Thu, 13 Aug 2020 11:48:02 -0700
Subject: [PATCH 40/55] asynk: remove due to prolonged breakage

---
 pkgs/tools/networking/asynk/default.nix | 47 -------------------------
 pkgs/top-level/all-packages.nix         |  2 --
 2 files changed, 49 deletions(-)
 delete mode 100644 pkgs/tools/networking/asynk/default.nix

diff --git a/pkgs/tools/networking/asynk/default.nix b/pkgs/tools/networking/asynk/default.nix
deleted file mode 100644
index b37f21335016..000000000000
--- a/pkgs/tools/networking/asynk/default.nix
+++ /dev/null
@@ -1,47 +0,0 @@
-{ stdenv, fetchurl, python2, python2Packages, makeWrapper }:
-
-stdenv.mkDerivation rec {
-  version = "2.0.0";
-  pname = "ASynK";
-
-  src = fetchurl {
-    name = "${pname}-${version}.tar.gz";
-    url = "https://github.com/skarra/ASynK/archive/v${version}.tar.gz";
-    sha256 = "1bp30437mnls0kzm0525p3bg5nw9alpqrqhw186f6zp9i4y5znp1";
-  };
-
-  propagatedBuildInputs = with python2Packages;
-    [ python2 makeWrapper tornado requests dateutil
-      vobject gdata caldavclientlibrary-asynk ];
-
-  installPhase = ''
-    mkdir -p $out/bin $out/lib
-    cp asynk.py $out/bin/
-    cp state.init.json $out/
-    cp -R config $out/
-    cp lib/*.py $out/lib # */
-    cp -R lib/s $out/lib/
-    cp -R asynk $out/
-
-    substituteInPlace $out/bin/asynk.py \
-      --replace "ASYNK_BASE_DIR    = os.path.dirname(os.path.abspath(__file__))" "ASYNK_BASE_DIR    = \"$out\""
-
-    for file in `find $out/asynk -type f`; do
-      # Oh yeah, tab characters!
-      substituteInPlace $file \
-        --replace 'from   vobject        import vobject' 'from vobject import *' \
-        --replace 'from   vobject    import vobject' 'from vobject import *'
-    done
-
-    wrapProgram "$out/bin/asynk.py" \
-      --prefix PYTHONPATH : "$PYTHONPATH"
-  '';
-
-  meta = with stdenv.lib; {
-    homepage = "http://asynk.io/";
-    description = "Flexible contacts synchronization program";
-    license = licenses.agpl3;
-    maintainers = [ ];
-    platforms = platforms.unix;
-  };
-}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 0b8e2990b4e7..41e7af4c09da 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -2431,8 +2431,6 @@ in
 
   assh = callPackage ../tools/networking/assh { };
 
-  asynk = callPackage ../tools/networking/asynk { };
-
   b2sum = callPackage ../tools/security/b2sum {
     inherit (llvmPackages) openmp;
   };

From 6e4042d067dfe9309f50d22ffa307691c58e208f Mon Sep 17 00:00:00 2001
From: Michael Weiss <dev.primeos@gmail.com>
Date: Thu, 13 Aug 2020 21:08:06 +0200
Subject: [PATCH 41/55] gollum: 5.1 -> 5.1.1 (security, CVE-2020-14001)

This also fixes a potential security issue (reported by bundler-audit)
by updating kramdown to 2.3.0 for CVE-2020-14001 [0].

[0]: https://github.com/advisories/GHSA-mqm2-cgpr-p4m6
---
 pkgs/applications/misc/gollum/Gemfile.lock | 11 ++++++-----
 pkgs/applications/misc/gollum/gemset.nix   | 17 +++++++++--------
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/pkgs/applications/misc/gollum/Gemfile.lock b/pkgs/applications/misc/gollum/Gemfile.lock
index 018b902294fe..91096ddc9173 100644
--- a/pkgs/applications/misc/gollum/Gemfile.lock
+++ b/pkgs/applications/misc/gollum/Gemfile.lock
@@ -2,17 +2,17 @@ GEM
   remote: https://rubygems.org/
   specs:
     backports (3.18.1)
-    concurrent-ruby (1.1.6)
+    concurrent-ruby (1.1.7)
     crass (1.0.6)
     execjs (2.7.0)
     ffi (1.13.1)
     gemojione (4.3.3)
       json
     github-markup (3.0.4)
-    gollum (5.1)
+    gollum (5.1.1)
       gemojione (~> 4.1)
       gollum-lib (~> 5.0)
-      kramdown (~> 2.1.0)
+      kramdown (~> 2.3)
       kramdown-parser-gfm (~> 1.0.0)
       mustache (>= 0.99.5, < 1.0.0)
       octicons (~> 8.5)
@@ -38,7 +38,8 @@ GEM
       mime-types (>= 1.15)
       rugged (~> 0.99)
     json (2.3.1)
-    kramdown (2.1.0)
+    kramdown (2.3.0)
+      rexml
     kramdown-parser-gfm (1.0.1)
       kramdown (~> 2.0)
     loofah (2.6.0)
@@ -63,7 +64,7 @@ GEM
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rexml (3.2.4)
-    rouge (3.21.0)
+    rouge (3.22.0)
     rss (0.2.9)
       rexml
     ruby2_keywords (0.0.2)
diff --git a/pkgs/applications/misc/gollum/gemset.nix b/pkgs/applications/misc/gollum/gemset.nix
index d7f837ed1fc3..45bf0e04d07f 100644
--- a/pkgs/applications/misc/gollum/gemset.nix
+++ b/pkgs/applications/misc/gollum/gemset.nix
@@ -14,10 +14,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "094387x4yasb797mv07cs3g6f08y56virc2rjcpb1k79rzaj3nhl";
+      sha256 = "1vnxrbhi7cq3p4y2v9iwd10v1c7l15is4var14hwnb2jip4fyjzz";
       type = "gem";
     };
-    version = "1.1.6";
+    version = "1.1.7";
   };
   crass = {
     groups = ["default"];
@@ -76,10 +76,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "06qc6flb2sik64ich3j4a9yky9cqsj77vdjff51wxi4lhd9ga6sk";
+      sha256 = "14i6y3ilv9l7cqvkawl75js26cfj1pd8cphhmq9lic95ajvdf371";
       type = "gem";
     };
-    version = "5.1";
+    version = "5.1.1";
   };
   gollum-lib = {
     dependencies = ["gemojione" "github-markup" "gollum-rugged_adapter" "loofah" "nokogiri" "octicons" "rouge" "twitter-text"];
@@ -114,14 +114,15 @@
     version = "2.3.1";
   };
   kramdown = {
+    dependencies = ["rexml"];
     groups = ["default"];
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1dl840bvx8d9nq6lg3mxqyvbiqnr6lk3jfsm6r8zhz7p5srmd688";
+      sha256 = "1vmw752c26ny2jwl0npn0gbyqwgz4hdmlpxnsld9qi9xhk5b1qh7";
       type = "gem";
     };
-    version = "2.1.0";
+    version = "2.3.0";
   };
   kramdown-parser-gfm = {
     dependencies = ["kramdown"];
@@ -286,10 +287,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1agrrmj88k9jkk36ra1ml2c1jffpp595pkxmcla74ac9ia09vn3s";
+      sha256 = "1wcz7i009wdbymlfsamagqi18m6ih8j60bii0k18f21g70r72i0m";
       type = "gem";
     };
-    version = "3.21.0";
+    version = "3.22.0";
   };
   rss = {
     dependencies = ["rexml"];

From f08049e712e661503e3bbfffbea81a0efddab573 Mon Sep 17 00:00:00 2001
From: Aaron Andersen <aaron@fosslib.net>
Date: Tue, 11 Aug 2020 22:04:16 -0400
Subject: [PATCH 42/55] nixos/mysql: move ExecStartPost into postStart

---
 nixos/modules/services/databases/mysql.nix | 208 ++++++++++-----------
 1 file changed, 102 insertions(+), 106 deletions(-)

diff --git a/nixos/modules/services/databases/mysql.nix b/nixos/modules/services/databases/mysql.nix
index c1a6b895bdd1..7d0a3f9afc48 100644
--- a/nixos/modules/services/databases/mysql.nix
+++ b/nixos/modules/services/databases/mysql.nix
@@ -375,118 +375,114 @@ in
           fi
         '';
 
+        postStart = let
+          # The super user account to use on *first* run of MySQL server
+          superUser = if isMariaDB then cfg.user else "root";
+        in ''
+          ${optionalString (!hasNotify) ''
+            # Wait until the MySQL server is available for use
+            count=0
+            while [ ! -e /run/mysqld/mysqld.sock ]
+            do
+                if [ $count -eq 30 ]
+                then
+                    echo "Tried 30 times, giving up..."
+                    exit 1
+                fi
+
+                echo "MySQL daemon not yet started. Waiting for 1 second..."
+                count=$((count++))
+                sleep 1
+            done
+          ''}
+
+          if [ -f ${cfg.dataDir}/mysql_init ]
+          then
+              # While MariaDB comes with a 'mysql' super user account since 10.4.x, MySQL does not
+              # Since we don't want to run this service as 'root' we need to ensure the account exists on first run
+              ( echo "CREATE USER IF NOT EXISTS '${cfg.user}'@'localhost' IDENTIFIED WITH ${if isMariaDB then "unix_socket" else "auth_socket"};"
+                echo "GRANT ALL PRIVILEGES ON *.* TO '${cfg.user}'@'localhost' WITH GRANT OPTION;"
+              ) | ${cfg.package}/bin/mysql -u ${superUser} -N
+
+              ${concatMapStrings (database: ''
+                # Create initial databases
+                if ! test -e "${cfg.dataDir}/${database.name}"; then
+                    echo "Creating initial database: ${database.name}"
+                    ( echo 'create database `${database.name}`;'
+
+                      ${optionalString (database.schema != null) ''
+                      echo 'use `${database.name}`;'
+
+                      # TODO: this silently falls through if database.schema does not exist,
+                      # we should catch this somehow and exit, but can't do it here because we're in a subshell.
+                      if [ -f "${database.schema}" ]
+                      then
+                          cat ${database.schema}
+                      elif [ -d "${database.schema}" ]
+                      then
+                          cat ${database.schema}/mysql-databases/*.sql
+                      fi
+                      ''}
+                    ) | ${cfg.package}/bin/mysql -u ${superUser} -N
+                fi
+              '') cfg.initialDatabases}
+
+              ${optionalString (cfg.replication.role == "master")
+                ''
+                  # Set up the replication master
+
+                  ( echo "use mysql;"
+                    echo "CREATE USER '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}' IDENTIFIED WITH mysql_native_password;"
+                    echo "SET PASSWORD FOR '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}' = PASSWORD('${cfg.replication.masterPassword}');"
+                    echo "GRANT REPLICATION SLAVE ON *.* TO '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}';"
+                  ) | ${cfg.package}/bin/mysql -u ${superUser} -N
+                ''}
+
+              ${optionalString (cfg.replication.role == "slave")
+                ''
+                  # Set up the replication slave
+
+                  ( echo "stop slave;"
+                    echo "change master to master_host='${cfg.replication.masterHost}', master_user='${cfg.replication.masterUser}', master_password='${cfg.replication.masterPassword}';"
+                    echo "start slave;"
+                  ) | ${cfg.package}/bin/mysql -u ${superUser} -N
+                ''}
+
+              ${optionalString (cfg.initialScript != null)
+                ''
+                  # Execute initial script
+                  # using toString to avoid copying the file to nix store if given as path instead of string,
+                  # as it might contain credentials
+                  cat ${toString cfg.initialScript} | ${cfg.package}/bin/mysql -u ${superUser} -N
+                ''}
+
+              rm ${cfg.dataDir}/mysql_init
+          fi
+
+          ${optionalString (cfg.ensureDatabases != []) ''
+            (
+            ${concatMapStrings (database: ''
+              echo "CREATE DATABASE IF NOT EXISTS \`${database}\`;"
+            '') cfg.ensureDatabases}
+            ) | ${cfg.package}/bin/mysql -N
+          ''}
+
+          ${concatMapStrings (user:
+            ''
+              ( echo "CREATE USER IF NOT EXISTS '${user.name}'@'localhost' IDENTIFIED WITH ${if isMariaDB then "unix_socket" else "auth_socket"};"
+                ${concatStringsSep "\n" (mapAttrsToList (database: permission: ''
+                  echo "GRANT ${permission} ON ${database} TO '${user.name}'@'localhost';"
+                '') user.ensurePermissions)}
+              ) | ${cfg.package}/bin/mysql -N
+            '') cfg.ensureUsers}
+        '';
+
         serviceConfig = {
           Type = if hasNotify then "notify" else "simple";
           Restart = "on-abort";
           RestartSec = "5s";
           # The last two environment variables are used for starting Galera clusters
           ExecStart = "${cfg.package}/bin/mysqld --defaults-file=/etc/my.cnf ${mysqldOptions} $_WSREP_NEW_CLUSTER $_WSREP_START_POSITION";
-          ExecStartPost =
-            let
-              # The super user account to use on *first* run of MySQL server
-              superUser = if isMariaDB then cfg.user else "root";
-              setupScript = pkgs.writeScript "mysql-setup" ''
-                #!${pkgs.runtimeShell} -e
-
-                ${optionalString (!hasNotify) ''
-                  # Wait until the MySQL server is available for use
-                  count=0
-                  while [ ! -e /run/mysqld/mysqld.sock ]
-                  do
-                      if [ $count -eq 30 ]
-                      then
-                          echo "Tried 30 times, giving up..."
-                          exit 1
-                      fi
-
-                      echo "MySQL daemon not yet started. Waiting for 1 second..."
-                      count=$((count++))
-                      sleep 1
-                  done
-                ''}
-
-                if [ -f ${cfg.dataDir}/mysql_init ]
-                then
-                    # While MariaDB comes with a 'mysql' super user account since 10.4.x MySQL does not
-                    # Since we don't want to run this service as 'root' we need to ensure the account exists on first run
-                    ( echo "CREATE USER IF NOT EXISTS '${cfg.user}'@'localhost' IDENTIFIED WITH ${if isMariaDB then "unix_socket" else "auth_socket"};"
-                      echo "GRANT ALL PRIVILEGES ON *.* TO '${cfg.user}'@'localhost' WITH GRANT OPTION;"
-                    ) | ${cfg.package}/bin/mysql -u ${superUser} -N
-
-                    ${concatMapStrings (database: ''
-                      # Create initial databases
-                      if ! test -e "${cfg.dataDir}/${database.name}"; then
-                          echo "Creating initial database: ${database.name}"
-                          ( echo 'create database `${database.name}`;'
-
-                            ${optionalString (database.schema != null) ''
-                            echo 'use `${database.name}`;'
-
-                            # TODO: this silently falls through if database.schema does not exist,
-                            # we should catch this somehow and exit, but can't do it here because we're in a subshell.
-                            if [ -f "${database.schema}" ]
-                            then
-                                cat ${database.schema}
-                            elif [ -d "${database.schema}" ]
-                            then
-                                cat ${database.schema}/mysql-databases/*.sql
-                            fi
-                            ''}
-                          ) | ${cfg.package}/bin/mysql -u ${superUser} -N
-                      fi
-                    '') cfg.initialDatabases}
-
-                    ${optionalString (cfg.replication.role == "master")
-                      ''
-                        # Set up the replication master
-
-                        ( echo "use mysql;"
-                          echo "CREATE USER '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}' IDENTIFIED WITH mysql_native_password;"
-                          echo "SET PASSWORD FOR '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}' = PASSWORD('${cfg.replication.masterPassword}');"
-                          echo "GRANT REPLICATION SLAVE ON *.* TO '${cfg.replication.masterUser}'@'${cfg.replication.slaveHost}';"
-                        ) | ${cfg.package}/bin/mysql -u ${superUser} -N
-                      ''}
-
-                    ${optionalString (cfg.replication.role == "slave")
-                      ''
-                        # Set up the replication slave
-
-                        ( echo "stop slave;"
-                          echo "change master to master_host='${cfg.replication.masterHost}', master_user='${cfg.replication.masterUser}', master_password='${cfg.replication.masterPassword}';"
-                          echo "start slave;"
-                        ) | ${cfg.package}/bin/mysql -u ${superUser} -N
-                      ''}
-
-                    ${optionalString (cfg.initialScript != null)
-                      ''
-                        # Execute initial script
-                        # using toString to avoid copying the file to nix store if given as path instead of string,
-                        # as it might contain credentials
-                        cat ${toString cfg.initialScript} | ${cfg.package}/bin/mysql -u ${superUser} -N
-                      ''}
-
-                    rm ${cfg.dataDir}/mysql_init
-                fi
-
-                ${optionalString (cfg.ensureDatabases != []) ''
-                  (
-                  ${concatMapStrings (database: ''
-                    echo "CREATE DATABASE IF NOT EXISTS \`${database}\`;"
-                  '') cfg.ensureDatabases}
-                  ) | ${cfg.package}/bin/mysql -N
-                ''}
-
-                ${concatMapStrings (user:
-                  ''
-                    ( echo "CREATE USER IF NOT EXISTS '${user.name}'@'localhost' IDENTIFIED WITH ${if isMariaDB then "unix_socket" else "auth_socket"};"
-                      ${concatStringsSep "\n" (mapAttrsToList (database: permission: ''
-                        echo "GRANT ${permission} ON ${database} TO '${user.name}'@'localhost';"
-                      '') user.ensurePermissions)}
-                    ) | ${cfg.package}/bin/mysql -N
-                  '') cfg.ensureUsers}
-              '';
-            in
-              "${setupScript}";
           # User and group
           User = cfg.user;
           Group = cfg.group;

From 806253800ba72152e9f12c9f2fd1e97a3ebecbe8 Mon Sep 17 00:00:00 2001
From: Aaron Andersen <aaron@fosslib.net>
Date: Wed, 12 Aug 2020 07:50:24 -0400
Subject: [PATCH 43/55] nixos/mysql: update release notes

---
 nixos/doc/manual/release-notes/rl-2009.xml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/nixos/doc/manual/release-notes/rl-2009.xml b/nixos/doc/manual/release-notes/rl-2009.xml
index 35ffadc17c5b..3a0c1865a624 100644
--- a/nixos/doc/manual/release-notes/rl-2009.xml
+++ b/nixos/doc/manual/release-notes/rl-2009.xml
@@ -109,6 +109,17 @@ systemd.services.mysql.serviceConfig.ProtectHome = lib.mkForce "read-only";
 systemd.services.mysql.serviceConfig.ReadWritePaths = [ "/var/data" ];
 </programlisting>
     </para>
+    <para>
+      The MySQL service no longer runs its <literal>systemd</literal> service startup script as <literal>root</literal> anymore. A dedicated non <literal>root</literal>
+      super user account is required for operation. This means users with an existing MySQL or MariaDB database server are required to run the following SQL statements
+      as a super admin user before upgrading:
+<programlisting>
+CREATE USER IF NOT EXISTS 'mysql'@'localhost' identified with unix_socket;
+GRANT ALL PRIVILEGES ON *.* TO 'mysql'@'localhost' WITH GRANT OPTION;
+</programlisting>
+      If you use MySQL instead of MariaDB please replace <literal>unix_socket</literal> with <literal>auth_socket</literal>. If you have changed the value of <xref linkend="opt-services.mysql.user"/>
+      from the default of <literal>mysql</literal> to a different user please change <literal>'mysql'@'localhost'</literal> to the corresponding user instead.
+    </para>
    </listitem>
    <listitem>
     <para>

From 6a4339974726bb78dc9f59d54859087ee5fbd429 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daniel=20=C8=98erb=C4=83nescu?= <daniel@serbanescu.dk>
Date: Thu, 13 Aug 2020 22:52:41 +0200
Subject: [PATCH 44/55] reportlab: 3.5.46 -> 3.5.47

---
 pkgs/development/python-modules/reportlab/default.nix | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/python-modules/reportlab/default.nix b/pkgs/development/python-modules/reportlab/default.nix
index 8463feca219a..a7c96ef2e6ed 100644
--- a/pkgs/development/python-modules/reportlab/default.nix
+++ b/pkgs/development/python-modules/reportlab/default.nix
@@ -11,11 +11,11 @@ let
   ft = freetype.overrideAttrs (oldArgs: { dontDisableStatic = true; });
 in buildPythonPackage rec {
   pname = "reportlab";
-  version = "3.5.46";
+  version = "3.5.47";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "56d71b78e7e4bb31a93e1dff13c22d19b7fb3890b021a39b6c3661b095bd7de8";
+    sha256 = "0gw0902yjszwxk0air69in7nk4h2q36r96ga3r4bz0p0cnmagcj5";
   };
 
   checkInputs = [ glibcLocales ];
@@ -30,6 +30,7 @@ in buildPythonPackage rec {
 
     # Remove the tests that require Vera fonts installed
     rm tests/test_graphics_render.py
+    rm tests/test_graphics_charts.py
   '';
 
   checkPhase = ''

From 961aa3145599bb7f44afb2eff9667c7ba5d28159 Mon Sep 17 00:00:00 2001
From: zowoq <59103226+zowoq@users.noreply.github.com>
Date: Wed, 12 Aug 2020 19:33:03 +1000
Subject: [PATCH 45/55] buildGoModule: update deleteVendor docs

---
 doc/languages-frameworks/go.xml                 | 9 ++++++++-
 pkgs/development/go-modules/generic/default.nix | 2 +-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/doc/languages-frameworks/go.xml b/doc/languages-frameworks/go.xml
index eee4706e5519..26414f23c7d2 100644
--- a/doc/languages-frameworks/go.xml
+++ b/doc/languages-frameworks/go.xml
@@ -40,7 +40,9 @@ pet = buildGoModule rec {
 
   subPackages = [ "." ]; <co xml:id='ex-buildGoModule-2' />
 
-  runVend = true; <co xml:id='ex-buildGoModule-3' />
+  deleteVendor = true; <co xml:id='ex-buildGoModule-3' />
+
+  runVend = true; <co xml:id='ex-buildGoModule-4' />
 
   meta = with lib; {
     description = "Simple command-line snippet manager, written in Go";
@@ -67,6 +69,11 @@ pet = buildGoModule rec {
      </para>
     </callout>
     <callout arearefs='ex-buildGoModule-3'>
+     <para>
+      <varname>deleteVendor</varname> removes the pre-existing vendor directory and fetches the dependencies. This should only be used if the dependencies included in the vendor folder are broken or incomplete.
+     </para>
+    </callout>
+    <callout arearefs='ex-buildGoModule-4'>
      <para>
       <varname>runVend</varname> runs the vend command to generate the vendor directory. This is useful if your code depends on c code and go mod tidy does not include the needed sources to build.
      </para>
diff --git a/pkgs/development/go-modules/generic/default.nix b/pkgs/development/go-modules/generic/default.nix
index 25b031a8229d..020f22ecd339 100644
--- a/pkgs/development/go-modules/generic/default.nix
+++ b/pkgs/development/go-modules/generic/default.nix
@@ -89,7 +89,7 @@ let
       fi
 
       if [ -e vendor ]; then
-        echo "vendor folder exists, please set 'vendorSha256=null;' or 'deleteVendor=true;' in your expression"
+        echo "vendor folder exists, please set 'vendorSha256 = null;' in your expression"
         exit 10
       fi
 

From cdd4547867c80bb6ced21d3800d06907090104be Mon Sep 17 00:00:00 2001
From: zowoq <59103226+zowoq@users.noreply.github.com>
Date: Wed, 12 Aug 2020 20:14:58 +1000
Subject: [PATCH 46/55] buildGoModule: check if vendor exists with deleteVendor

---
 pkgs/development/go-modules/generic/default.nix | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/go-modules/generic/default.nix b/pkgs/development/go-modules/generic/default.nix
index 020f22ecd339..c15502387211 100644
--- a/pkgs/development/go-modules/generic/default.nix
+++ b/pkgs/development/go-modules/generic/default.nix
@@ -85,10 +85,15 @@ let
       runHook preBuild
 
       if [ ${deleteFlag} == "true" ]; then
-        rm -rf vendor
+        if [ ! -d vendor ]; then
+          echo "vendor folder does not exist, 'deleteVendor' is not needed"
+          exit 10
+        else
+          rm -rf vendor
+        fi
       fi
 
-      if [ -e vendor ]; then
+      if [ -d vendor ]; then
         echo "vendor folder exists, please set 'vendorSha256 = null;' in your expression"
         exit 10
       fi

From 465646f12e91e93988739021093d1def7748d3b2 Mon Sep 17 00:00:00 2001
From: zowoq <59103226+zowoq@users.noreply.github.com>
Date: Wed, 12 Aug 2020 08:25:46 +1000
Subject: [PATCH 47/55] .github/CODEOWNERS: add go compilers and builders

---
 .github/CODEOWNERS | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 4be9ae506ea1..d362d857838b 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -202,3 +202,8 @@
 
 # Blockchains
 /pkgs/applications/blockchains  @mmahut
+
+# Go
+/pkgs/development/compilers/go @kalbasit @Mic92 @zowoq
+/pkgs/development/go-modules   @kalbasit @Mic92 @zowoq
+/pkgs/development/go-packages  @kalbasit @Mic92 @zowoq

From 6bb4cca85755efc64acb509977265860a3620a6a Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 23:29:21 +0000
Subject: [PATCH 48/55] fatsort: 1.6.2.605 -> 1.6.3.622

---
 pkgs/tools/filesystems/fatsort/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/filesystems/fatsort/default.nix b/pkgs/tools/filesystems/fatsort/default.nix
index b8f63a379b1b..90ab3a6df415 100644
--- a/pkgs/tools/filesystems/fatsort/default.nix
+++ b/pkgs/tools/filesystems/fatsort/default.nix
@@ -1,12 +1,12 @@
 {stdenv, fetchurl, help2man}:
 
 stdenv.mkDerivation rec {
-  version = "1.6.2.605";
+  version = "1.6.3.622";
   pname = "fatsort";
 
   src = fetchurl {
     url = "mirror://sourceforge/fatsort/${pname}-${version}.tar.xz";
-    sha256 = "1dzzsl3a1ampari424vxkma0i87qkbgkgm2169x9xf3az0vgmjh8";
+    sha256 = "1z2nabm38lg56h05yx3jjsndbqxk1zbjcisrczzamypn13m98728";
   };
 
   patches = [ ./fatsort-Makefiles.patch ];

From 20fab51c3f02d908172d9a67dbff7840ff5f5b86 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Thu, 13 Aug 2020 23:50:47 +0000
Subject: [PATCH 49/55] gitolite: 3.6.11 -> 3.6.12

---
 pkgs/applications/version-management/gitolite/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/version-management/gitolite/default.nix b/pkgs/applications/version-management/gitolite/default.nix
index 60fed6954dc5..d0853f339786 100644
--- a/pkgs/applications/version-management/gitolite/default.nix
+++ b/pkgs/applications/version-management/gitolite/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "gitolite";
-  version = "3.6.11";
+  version = "3.6.12";
 
   src = fetchFromGitHub {
     owner = "sitaramc";
     repo = "gitolite";
     rev = "v${version}";
-    sha256 = "1rkj7gknwjlc5ij9w39zf5mr647bm45la57yjczydmvrb8c56yrh";
+    sha256 = "05xw1pmagvkrbzga5pgl3xk9qyc6b5x73f842454f3w9ijspa8zy";
   };
 
   buildInputs = [ nettools perl ];

From 5c3ca833081391f1d2f6f205263ac8498fe7762a Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Fri, 14 Aug 2020 00:01:35 +0000
Subject: [PATCH 50/55] fping: 4.4 -> 5.0

---
 pkgs/tools/networking/fping/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/networking/fping/default.nix b/pkgs/tools/networking/fping/default.nix
index f7e1f7ce0d35..d170ee4cd0e3 100644
--- a/pkgs/tools/networking/fping/default.nix
+++ b/pkgs/tools/networking/fping/default.nix
@@ -1,11 +1,11 @@
 { stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  name = "fping-4.4";
+  name = "fping-5.0";
 
   src = fetchurl {
     url = "https://www.fping.org/dist/${name}.tar.gz";
-    sha256 = "049dnyr6d869kwrnfhkj3afifs3219fy6hv7kmsb3irdlmjlp1cz";
+    sha256 = "1f2prmii4fyl44cfykp40hp4jjhicrhddh9v3dfs11j6nsww0f7d";
   };
 
   configureFlags = [ "--enable-ipv6" "--enable-ipv4" ];

From 11fceef0d47d11cacecc699ad10934404636b4e6 Mon Sep 17 00:00:00 2001
From: "Wael M. Nasreddine" <wael.nasreddine@gmail.com>
Date: Thu, 13 Aug 2020 18:49:42 -0700
Subject: [PATCH 51/55] brave: 1.11.97 -> 1.12.112

---
 pkgs/applications/networking/browsers/brave/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/networking/browsers/brave/default.nix b/pkgs/applications/networking/browsers/brave/default.nix
index 5a8171a40a4e..ceceffb8da08 100644
--- a/pkgs/applications/networking/browsers/brave/default.nix
+++ b/pkgs/applications/networking/browsers/brave/default.nix
@@ -86,11 +86,11 @@ in
 
 stdenv.mkDerivation rec {
   pname = "brave";
-  version = "1.11.97";
+  version = "1.12.112";
 
   src = fetchurl {
     url = "https://github.com/brave/brave-browser/releases/download/v${version}/brave-browser_${version}_amd64.deb";
-    sha256 = "1wmjwk98fvzy5slyqpzpnn1mx663q3pvcyr3fzcinf6v971vz3q2";
+    sha256 = "0nvxmz1wrr6cfyhbnrfjsy9szbjmvjl6080pgkp25xa8rcql5gmb";
   };
 
   dontConfigure = true;

From 1aba5fcb4afd55fd26161608aa1f517b2f7351f0 Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Fri, 14 Aug 2020 01:53:35 +0000
Subject: [PATCH 52/55] s3fs: 1.86 -> 1.87

---
 pkgs/tools/filesystems/s3fs/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/filesystems/s3fs/default.nix b/pkgs/tools/filesystems/s3fs/default.nix
index 282252b4b13a..3e91a1b0c475 100644
--- a/pkgs/tools/filesystems/s3fs/default.nix
+++ b/pkgs/tools/filesystems/s3fs/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "s3fs-fuse";
-  version = "1.86";
+  version = "1.87";
 
   src = fetchFromGitHub {
     owner  = "s3fs-fuse";
     repo   = "s3fs-fuse";
     rev    = "v${version}";
-    sha256 = "115zqbspr17xmidhizjmsqv9c7ql2jhmxws8wh59bpz2335kn0q7";
+    sha256 = "09ib3sh6vg3z7cpccj3ysgpdyf84a98lf6nz15a61r4l27h111f2";
   };
 
   buildInputs = [ curl openssl libxml2 ]

From 551147ab22af54d641b70e2bff8056b12f355dcc Mon Sep 17 00:00:00 2001
From: "R. RyanTM" <ryantm-bot@ryantm.com>
Date: Fri, 14 Aug 2020 03:47:36 +0000
Subject: [PATCH 53/55] html-xml-utils: 7.8 -> 7.9

---
 pkgs/tools/text/xml/html-xml-utils/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/tools/text/xml/html-xml-utils/default.nix b/pkgs/tools/text/xml/html-xml-utils/default.nix
index c42ecfc24410..d4bd40a11993 100644
--- a/pkgs/tools/text/xml/html-xml-utils/default.nix
+++ b/pkgs/tools/text/xml/html-xml-utils/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "html-xml-utils";
-  version = "7.8";
+  version = "7.9";
 
   src = fetchurl {
     url = "https://www.w3.org/Tools/HTML-XML-utils/${pname}-${version}.tar.gz";
-    sha256 = "0p8df3c6mw879vdi8l63kbdqylkf1is10b067mh9kipgfy91rd4s";
+    sha256 = "0gs3xvdbzhk5k12i95p5d4fgkkaldnlv45sch7pnncb0lrpcjsnq";
   };
 
   buildInputs = [curl libiconv];

From 49a99103c83bc5dc46576834f575a400b1940a4f Mon Sep 17 00:00:00 2001
From: Vincent Laporte <Vincent.Laporte@gmail.com>
Date: Tue, 11 Aug 2020 07:13:56 +0200
Subject: [PATCH 54/55] =?UTF-8?q?ocamlPackages.uucd:=2010.0.0=20=E2=86=92?=
 =?UTF-8?q?=2013.0.0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pkgs/development/ocaml-modules/uucd/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/development/ocaml-modules/uucd/default.nix b/pkgs/development/ocaml-modules/uucd/default.nix
index 097676e8abba..355b177b204f 100644
--- a/pkgs/development/ocaml-modules/uucd/default.nix
+++ b/pkgs/development/ocaml-modules/uucd/default.nix
@@ -6,11 +6,11 @@ let
 in
 stdenv.mkDerivation rec {
   name = "ocaml-${pname}-${version}";
-  version = "10.0.0";
+  version = "13.0.0";
 
   src = fetchurl {
     url = "${webpage}/releases/${pname}-${version}.tbz";
-    sha256 = "0cdyg6vaic4n58w80qriwvaq1c40ng3fh74ilxrwajbq163k055q";
+    sha256 = "1fg77hg4ibidkv1x8hhzl8z3rzmyymn8m4i35jrdibb8adigi8v2";
   };
 
   buildInputs = [ ocaml findlib ocamlbuild topkg ];

From c25d99efcb49408f0ceb402a400409af055e4bfb Mon Sep 17 00:00:00 2001
From: Vincent Laporte <Vincent.Laporte@gmail.com>
Date: Fri, 7 Aug 2020 10:31:59 +0200
Subject: [PATCH 55/55] =?UTF-8?q?ocamlPackages.merlin-extend:=200.4=20?=
 =?UTF-8?q?=E2=86=92=200.6?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../ocaml-modules/merlin-extend/default.nix        | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/pkgs/development/ocaml-modules/merlin-extend/default.nix b/pkgs/development/ocaml-modules/merlin-extend/default.nix
index ad3b1337977f..752fbc039fa2 100644
--- a/pkgs/development/ocaml-modules/merlin-extend/default.nix
+++ b/pkgs/development/ocaml-modules/merlin-extend/default.nix
@@ -1,20 +1,18 @@
-{ lib, buildDunePackage, fetchFromGitHub, cppo }:
+{ lib, buildDunePackage, fetchurl, cppo }:
 
 buildDunePackage rec {
   pname = "merlin-extend";
-  version = "0.4";
+  version = "0.6";
 
-  src = fetchFromGitHub {
-    owner = "let-def";
-    repo = pname;
-    sha256 = "1dxiqmm7ry24gvw6p9n4mrz37mnq4s6m8blrccsv3rb8yq82acx9";
-    rev = "v${version}";
+  src = fetchurl {
+    url = "https://github.com/let-def/merlin-extend/releases/download/v${version}/merlin-extend-v${version}.tbz";
+    sha256 = "0hvc4mz92x3rl2dxwrhvhzwl4gilnyvvwcqgr45vmdpyjyp3dwn2";
   };
 
   buildInputs = [ cppo ];
 
   meta = with lib; {
-    inherit (src.meta) homepage;
+    homepage = "https://github.com/let-def/merlin-extend";
     description = "SDK to extend Merlin";
     license = licenses.mit;
     maintainers = [ maintainers.volth ];