various: refactor and move to pkgs/by-name (#491903)

pkgs/by-name/ap/apache-jena-fuseki/package.nix

@@ -2,7 +2,7 @@
   lib,
   stdenv,
   fetchurl,
-  java,
+  jre,
   coreutils,
   which,
   makeWrapper,
@@ -28,7 +28,7 @@ stdenv.mkDerivation rec {
       # It is necessary to set the default $FUSEKI_BASE directory to a writable location
       # By default it points to $FUSEKI_HOME/run which is in the nix store
       wrapProgram "$i" \
-        --prefix "PATH" : "${java}/bin/:${coreutils}/bin:${which}/bin" \
+        --prefix "PATH" : "${jre}/bin/:${coreutils}/bin:${which}/bin" \
         --set-default "FUSEKI_HOME" "$out" \
         --run "if [ -z \"\$FUSEKI_BASE\" ]; then export FUSEKI_BASE=\"\$HOME/.local/fuseki\" ; mkdir -p \"\$HOME/.local/fuseki\" ; fi" \
         ;
@@ -36,7 +36,7 @@ stdenv.mkDerivation rec {
   '';
   passthru = {
     tests = {
-      basic-test = pkgs.callPackage ./fuseki-test.nix { };
+      basic-test = pkgs.callPackage ./basic-test.nix { };
     };
   };
   meta = {

pkgs/by-name/ap/apache-jena/package.nix

@@ -2,7 +2,7 @@
   lib,
   stdenv,
   fetchurl,
-  java,
+  jre,
   makeWrapper,
 }:
 
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
   installPhase = ''
     cp -r . "$out"
     for i in "$out"/bin/*; do
-      wrapProgram "$i" --prefix "PATH" : "${java}/bin/"
+      wrapProgram "$i" --prefix "PATH" : "${jre}/bin/"
     done
   '';
   meta = {

pkgs/by-name/ic/icinga2-agent/package.nix

@@ -0,0 +1,8 @@
+{ icinga2 }:
+icinga2.override {
+  nameSuffix = "-agent";
+  withMysql = false;
+  withNotification = false;
+  withIcingadb = false;
+  withPerfdata = false;
+}

pkgs/by-name/ic/icinga2/package.nix

@@ -28,14 +28,14 @@
   nameSuffix ? "",
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "icinga2${nameSuffix}";
   version = "2.15.1";
 
   src = fetchFromGitHub {
     owner = "icinga";
     repo = "icinga2";
-    rev = "v${version}";
+    rev = "v${finalAttrs.version}";
     hash = "sha256-w/eD07yzBm3x4G74OuGwkmpBzj63UoklmcKxVi5lx8E=";
   };
 
@@ -118,9 +118,9 @@ stdenv.mkDerivation rec {
     ''}
   '';
 
-  vim = runCommand "vim-icinga2-${version}" { pname = "vim-icinga2"; } ''
+  vim = runCommand "vim-icinga2-${finalAttrs.version}" { pname = "vim-icinga2"; } ''
     mkdir -p $out/share/vim-plugins
-    cp -r "${src}/tools/syntax/vim" $out/share/vim-plugins/icinga2
+    cp -r "${finalAttrs.src}/tools/syntax/vim" $out/share/vim-plugins/icinga2
   '';
 
   meta = {
@@ -133,4 +133,4 @@ stdenv.mkDerivation rec {
       helsinki-Jo
     ];
   };
-}
+})

pkgs/by-name/in/influxdb/package.nix

@@ -24,7 +24,7 @@ let
     };
     patches = [
       # https://github.com/influxdata/flux/pull/5542
-      ../influxdb2/fix-unsigned-char.patch
+      ./fix-unsigned-char.patch
     ];
 
     # Don't fail on missing code documentation and allow dead_code/lifetime/unused_assignments warnings

pkgs/by-name/in/influxdb2-server/fix-unsigned-char.patch

@@ -0,0 +1,13 @@
+diff --git a/flux/src/cffi.rs b/flux/src/cffi.rs
+index ba18e3d5..0c1badf8 100644
+--- a/flux/src/cffi.rs
++++ b/flux/src/cffi.rs
+@@ -1149,7 +1149,7 @@ from(bucket: v.bucket)
+     fn parse_with_invalid_utf8() {
+         let cfname = CString::new("foo.flux").unwrap();
+         let cfname_ptr: *const c_char = cfname.as_ptr();
+-        let v: Vec<c_char> = vec![-61, 0];
++        let v: Vec<c_char> = vec![-61i8 as c_char, 0];
+         let csrc: *const c_char = &v[0];
+         // Safety: both pointers are valid
+         let pkg = unsafe { flux_parse(cfname_ptr, csrc) };

pkgs/by-name/in/influxdb2/package.nix

@@ -0,0 +1,16 @@
+# For backwards compatibility with older versions of influxdb2,
+# which bundled the server and CLI into the same derivation. Will be
+# removed in a few releases.
+# - David Anderson 2021-12-16 in 84bc3a02807fd
+{
+  buildEnv,
+  influxdb2-server,
+  influxdb2-cli,
+}:
+buildEnv {
+  name = "influxdb2";
+  paths = [
+    influxdb2-server
+    influxdb2-cli
+  ];
+}

pkgs/by-name/ma/mastodon/package.nix

@@ -1,15 +1,15 @@
 {
   lib,
   stdenv,
-  nodejs-slim,
+  nodejs-slim_22,
   bundlerEnv,
   nixosTests,
-  yarn-berry,
+  yarn-berry_4,
   callPackage,
-  ruby,
+  ruby_3_3,
   writeShellScript,
   brotli,
-  python3,
+  python311,
 
   # Allow building a fork or custom version of Mastodon:
   pname ? "mastodon",
@@ -21,6 +21,12 @@
   yarnHash ? srcOverride.yarnHash,
   yarnMissingHashes ? srcOverride.yarnMissingHashes,
 }:
+let
+  nodejs-slim = nodejs-slim_22;
+  python3 = python311;
+  ruby = ruby_3_3;
+  yarn-berry = yarn-berry_4.override { nodejs = nodejs-slim; };
+in
 
 stdenv.mkDerivation rec {
   inherit pname version;

pkgs/by-name/ma/mautrix-telegram/package.nix

@@ -23,14 +23,14 @@ let
     };
   };
 in
-python.pkgs.buildPythonPackage rec {
+python.pkgs.buildPythonPackage (finalAttrs: {
   pname = "mautrix-telegram";
   version = "0.15.3";
 
   src = fetchFromGitHub {
     owner = "mautrix";
     repo = "telegram";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-w3BqWyAJV/lZPoOFDzxhootpw451lYruwM9efwS6cEc=";
   };
 
@@ -90,4 +90,4 @@ python.pkgs.buildPythonPackage rec {
     ];
     mainProgram = "mautrix-telegram";
   };
-}
+})

pkgs/by-name/mo/mobilizon/package.nix

@@ -2,21 +2,22 @@
   lib,
   callPackage,
   writeShellScriptBin,
-  beamPackages,
+  beam,
   mix2nix,
   fetchFromGitHub,
   git,
   cmake,
   nixosTests,
   nixfmt,
-  mobilizon-frontend,
+  mobilizon-frontend ? callPackage ./frontend.nix { },
 }:
 
 let
-  inherit (beamPackages) mixRelease buildMix;
+  beamPackages = beam.packages.erlang_27.extend (self: super: { elixir = self.elixir_1_18; });
+
   common = callPackage ./common.nix { };
 in
-mixRelease rec {
+beamPackages.mixRelease rec {
   inherit (common) pname version src;
 
   # A typo that is a build failure on elixir 1.18
@@ -59,7 +60,7 @@ mixRelease rec {
         });
 
         # The remainder are Git dependencies (and their deps) that are not supported by mix2nix currently.
-        web_push_encryption = buildMix {
+        web_push_encryption = beamPackages.buildMix {
           name = "web_push_encryption";
           version = "0.3.1";
           src = fetchFromGitHub {
@@ -73,7 +74,7 @@ mixRelease rec {
             jose
           ];
         };
-        icalendar = buildMix rec {
+        icalendar = beamPackages.buildMix rec {
           name = "icalendar";
           version = "1.1.2";
           src = fetchFromGitHub {
@@ -88,7 +89,7 @@ mixRelease rec {
             timex
           ];
         };
-        rajska = buildMix rec {
+        rajska = beamPackages.buildMix rec {
           name = "rajska";
           version = "1.3.3";
           src = fetchFromGitHub {
@@ -106,7 +107,7 @@ mixRelease rec {
             mock
           ];
         };
-        exkismet = buildMix rec {
+        exkismet = beamPackages.buildMix rec {
           name = "exkismet";
           version = "0.0.3";
           src = fetchFromGitHub {

pkgs/by-name/ns/nsd/package.nix

@@ -7,34 +7,34 @@
   pkg-config,
   systemdMinimal,
   nixosTests,
-  bind8Stats ? false,
-  checking ? false,
-  ipv6 ? true,
-  mmap ? false,
-  minimalResponses ? true,
-  nsec3 ? true,
-  ratelimit ? false,
-  recvmmsg ? false,
-  rootServer ? false,
-  rrtypes ? false,
-  zoneStats ? false,
-  withSystemd ? lib.meta.availableOn stdenv.hostPlatform systemdMinimal,
-  configFile ? "/etc/nsd/nsd.conf",
+  config,
+  # set default options for config values
+  # maybe TODO: move these into a proper module
+  # (after https://github.com/NixOS/nixpkgs/pull/489889?)
+  bind8Stats ? config.nsd.bind8Stats or false,
+  checking ? config.nsd.checking or false,
+  ipv6 ? config.nsd.ipv6 or true,
+  mmap ? config.nsd.mmap or false,
+  minimalResponses ? config.nsd.minimalResponses or true,
+  nsec3 ? config.nsd.nsec3 or true,
+  ratelimit ? config.nsd.ratelimit or false,
+  recvmmsg ? config.nsd.recvmmsg or false,
+  rootServer ? config.nsd.rootServer or false,
+  rrtypes ? config.nsd.rrtypes or false,
+  zoneStats ? config.nsd.zoneStats or false,
+  withSystemd ? config.nsd.withSystemd or (lib.meta.availableOn stdenv.hostPlatform systemdMinimal),
+  configFile ? config.nsd.configFile or "/etc/nsd/nsd.conf",
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "nsd";
   version = "4.12.0";
 
   src = fetchurl {
-    url = "https://www.nlnetlabs.nl/downloads/${pname}/${pname}-${version}.tar.gz";
-    sha256 = "sha256-+ezCz3m6UFgPLfYpGO/EQAhMW/EQV9tEwZqpZDzUteg=";
+    url = "https://www.nlnetlabs.nl/downloads/nsd/nsd-${finalAttrs.version}.tar.gz";
+    hash = "sha256-+ezCz3m6UFgPLfYpGO/EQAhMW/EQV9tEwZqpZDzUteg=";
   };
 
-  prePatch = ''
-    substituteInPlace nsd-control-setup.sh.in --replace openssl ${openssl}/bin/openssl
-  '';
-
   nativeBuildInputs = lib.optionals withSystemd [
     pkg-config
   ];
@@ -49,6 +49,15 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  # TODO: prePatch doesn't actually get executed because patchPhase is overridden
+  prePatch = ''
+    substituteInPlace nsd-control-setup.sh.in --replace openssl ${openssl}/bin/openssl
+  '';
+
+  patchPhase = ''
+    sed 's@$(INSTALL_DATA) nsd.conf.sample $(DESTDIR)$(nsdconfigfile).sample@@g' -i Makefile.in
+  '';
+
   configureFlags =
     let
       edf = c: o: if c then [ "--enable-${o}" ] else [ "--disable-${o}" ];
@@ -72,10 +81,6 @@ stdenv.mkDerivation rec {
       "--with-configdir=etc/nsd"
     ];
 
-  patchPhase = ''
-    sed 's@$(INSTALL_DATA) nsd.conf.sample $(DESTDIR)$(nsdconfigfile).sample@@g' -i Makefile.in
-  '';
-
   passthru.tests = {
     inherit (nixosTests) nsd;
   };
@@ -86,4 +91,4 @@ stdenv.mkDerivation rec {
     license = lib.licenses.bsd3;
     platforms = lib.platforms.unix;
   };
-}
+})

pkgs/by-name/nu/nullmailer/package.nix

@@ -1,20 +1,17 @@
 {
-  stdenv,
+  gccStdenv,
   fetchurl,
   lib,
   tls ? true,
-  gnutls ? null,
+  gnutls,
 }:
 
-assert tls -> gnutls != null;
-
-stdenv.mkDerivation rec {
-
+gccStdenv.mkDerivation (finalAttrs: {
   version = "2.2";
   pname = "nullmailer";
 
   src = fetchurl {
-    url = "https://untroubled.org/nullmailer/nullmailer-${version}.tar.gz";
+    url = "https://untroubled.org/nullmailer/nullmailer-${finalAttrs.version}.tar.gz";
     sha256 = "0md8cf90fl2yf3zh9njjy42a673v4j4ygyq95xg7fzkygdigm1lq";
   };
 
@@ -55,4 +52,4 @@ stdenv.mkDerivation rec {
     platforms = lib.platforms.all;
     maintainers = [ ];
   };
-}
+})

pkgs/by-name/qp/qpaeq/package.nix

@@ -1,10 +1,10 @@
 {
-  stdenv,
-  wrapQtAppsHook,
-  makeDesktopItem,
-  python3,
   lib,
+  stdenv,
   pulseaudio,
+  makeDesktopItem,
+  qt5,
+  python3,
 }:
 
 let
@@ -26,17 +26,15 @@ stdenv.mkDerivation {
   pname = "qpaeq";
   inherit (pulseaudio) version src;
 
-  nativeBuildInputs = [ wrapQtAppsHook ];
+  nativeBuildInputs = [ qt5.wrapQtAppsHook ];
 
   buildInputs = [
-
     (python3.withPackages (
       ps: with ps; [
         pyqt5
         dbus-python
       ]
     ))
-
   ];
 
   dontBuild = true;

pkgs/by-name/re/rethinkdb/package.nix

@@ -1,27 +1,29 @@
 {
   lib,
-  stdenv,
+  clangStdenv,
   fetchurl,
   which,
   m4,
-  protobuf,
+  protobuf_21,
   boost,
   zlib,
   curl,
   openssl,
   icu,
   jemalloc,
-  libtool,
+  cctools,
   python3Packages,
   makeWrapper,
 }:
-
-stdenv.mkDerivation rec {
+let
+  stdenv = clangStdenv;
+in
+stdenv.mkDerivation (finalAttrs: {
   pname = "rethinkdb";
   version = "2.4.4";
 
   src = fetchurl {
-    url = "https://download.rethinkdb.com/repository/raw/dist/${pname}-${version}.tgz";
+    url = "https://download.rethinkdb.com/repository/raw/dist/rethinkdb-${finalAttrs.version}.tgz";
     hash = "sha256-UJEjdgK2KDDbLLParKarNGMjI3QeZxDC8N5NhPRCcR8=";
   };
 
@@ -44,7 +46,7 @@ stdenv.mkDerivation rec {
   makeFlags = [ "rethinkdb" ];
 
   buildInputs = [
-    protobuf
+    protobuf_21
     boost
     zlib
     curl
@@ -52,7 +54,7 @@ stdenv.mkDerivation rec {
     icu
   ]
   ++ lib.optional (!stdenv.hostPlatform.isDarwin) jemalloc
-  ++ lib.optional stdenv.hostPlatform.isDarwin libtool;
+  ++ lib.optional stdenv.hostPlatform.isDarwin cctools;
 
   nativeBuildInputs = [
     which
@@ -84,4 +86,4 @@ stdenv.mkDerivation rec {
       thoughtpolice
     ];
   };
-}
+})

pkgs/servers/nosql/influxdb2/combined.nix

@@ -1,12 +0,0 @@
-{
-  buildEnv,
-  influxdb2-server,
-  influxdb2-cli,
-}:
-buildEnv {
-  name = "influxdb2";
-  paths = [
-    influxdb2-server
-    influxdb2-cli
-  ];
-}

pkgs/top-level/all-packages.nix

@@ -1847,11 +1847,6 @@ with pkgs;
 
   mkspiffs-presets = recurseIntoAttrs (callPackages ../by-name/mk/mkspiffs/presets.nix { });
 
-  mobilizon = callPackage ../servers/mobilizon {
-    beamPackages = beam.packages.erlang_27.extend (self: super: { elixir = self.elixir_1_18; });
-    mobilizon-frontend = callPackage ../servers/mobilizon/frontend.nix { };
-  };
-
   nltk-data = recurseIntoAttrs (callPackage ../tools/text/nltk-data { });
 
   seabios-coreboot = seabios.override { ___build-type = "coreboot"; };
@@ -2770,8 +2765,6 @@ with pkgs;
 
   maubot = with python3Packages; toPythonApplication maubot;
 
-  mautrix-telegram = recurseIntoAttrs (callPackage ../servers/mautrix-telegram { });
-
   m2r = with python3Packages; toPythonApplication m2r;
 
   md2gemini = with python3.pkgs; toPythonApplication md2gemini;
@@ -3266,10 +3259,6 @@ with pkgs;
   playwright-driver = (callPackage ../development/web/playwright/driver.nix { }).playwright-core;
   playwright-test = (callPackage ../development/web/playwright/driver.nix { }).playwright-test;
 
-  plex = callPackage ../servers/plex { };
-
-  plexRaw = callPackage ../servers/plex/raw.nix { };
-
   tabview = with python3Packages; toPythonApplication tabview;
 
   inherit (callPackage ../development/tools/pnpm { })
@@ -8115,14 +8104,6 @@ with pkgs;
   };
   cassandra = cassandra_4;
 
-  apache-jena = callPackage ../servers/nosql/apache-jena/binary.nix {
-    java = jre;
-  };
-
-  apache-jena-fuseki = callPackage ../servers/nosql/apache-jena/fuseki-binary.nix {
-    java = jre;
-  };
-
   inherit (callPackages ../servers/asterisk { })
     asterisk
     asterisk-stable
@@ -8163,7 +8144,6 @@ with pkgs;
   freshrss = callPackage ../servers/web-apps/freshrss { };
   freshrss-extensions = recurseIntoAttrs (callPackage ../servers/web-apps/freshrss/extensions { });
 
-  grafana = callPackage ../servers/monitoring/grafana { };
   grafanaPlugins = recurseIntoAttrs (callPackages ../servers/monitoring/grafana/plugins { });
 
   inherit (callPackage ../servers/hbase { })
@@ -8244,10 +8224,6 @@ with pkgs;
     kanidmWithSecretProvisioning_1_9
     ;
 
-  leafnode = callPackage ../servers/news/leafnode { };
-
-  leafnode1 = callPackage ../servers/news/leafnode/1.nix { };
-
   lemmy-server = callPackage ../servers/web-apps/lemmy/server.nix { };
 
   lemmy-ui = callPackage ../servers/web-apps/lemmy/ui.nix {
@@ -8258,13 +8234,6 @@ with pkgs;
   inherit (mailmanPackages) mailman mailman-hyperkitty;
   mailman-web = mailmanPackages.web;
 
-  mastodon = callPackage ../servers/mastodon {
-    nodejs-slim = nodejs-slim_22;
-    python3 = python311;
-    ruby = ruby_3_3;
-    yarn-berry = yarn-berry_4.override { nodejs = nodejs-slim_22; };
-  };
-
   micro-full = micro.wrapper.override {
     extraPackages = [
       wl-clipboard
@@ -8343,8 +8312,6 @@ with pkgs;
     ];
   };
 
-  nsd = callPackage ../servers/dns/nsd (config.nsd or { });
-
   nsdiff = perlPackages.nsdiff;
 
   openafs = callPackage ../servers/openafs/1.8 { };
@@ -8359,12 +8326,6 @@ with pkgs;
 
   # PulseAudio daemons
 
-  hsphfpd = callPackage ../servers/pulseaudio/hsphfpd.nix { };
-
-  pulseaudio = callPackage ../servers/pulseaudio { };
-
-  qpaeq = libsForQt5.callPackage ../servers/pulseaudio/qpaeq.nix { };
-
   pulseaudioFull = pulseaudio.override {
     x11Support = true;
     jackaudioSupport = true;
@@ -8406,16 +8367,6 @@ with pkgs;
     boost = boost179.override { enableShared = false; };
   };
 
-  influxdb = callPackage ../servers/nosql/influxdb { };
-  influxdb2-server = callPackage ../servers/nosql/influxdb2 { };
-  influxdb2-cli = callPackage ../servers/nosql/influxdb2/cli.nix { };
-  influxdb2-token-manipulator = callPackage ../servers/nosql/influxdb2/token-manipulator.nix { };
-  influxdb2-provision = callPackage ../servers/nosql/influxdb2/provision.nix { };
-  # For backwards compatibility with older versions of influxdb2,
-  # which bundled the server and CLI into the same derivation. Will be
-  # removed in a few releases.
-  influxdb2 = callPackage ../servers/nosql/influxdb2/combined.nix { };
-
   mysql80 = callPackage ../servers/sql/mysql/8.0.x.nix {
     inherit (darwin) developer_cmds DarwinTools;
     boost = boost177; # Configure checks for specific version.
@@ -8431,16 +8382,6 @@ with pkgs;
     mir_2_15
     ;
 
-  icinga2 = callPackage ../servers/monitoring/icinga2 { };
-
-  icinga2-agent = callPackage ../servers/monitoring/icinga2 {
-    nameSuffix = "-agent";
-    withMysql = false;
-    withNotification = false;
-    withIcingadb = false;
-    withPerfdata = false;
-  };
-
   nagiosPlugins = recurseIntoAttrs (callPackages ../servers/monitoring/nagios-plugins { });
 
   qboot = pkgsi686Linux.callPackage ../applications/virtualization/qboot { };
@@ -8494,12 +8435,6 @@ with pkgs;
 
   pypiserver = with python3Packages; toPythonApplication pypiserver;
 
-  rethinkdb = callPackage ../servers/nosql/rethinkdb {
-    stdenv = clangStdenv;
-    libtool = cctools;
-    protobuf = protobuf_21;
-  };
-
   samba4 = callPackage ../servers/samba/4.x.nix { };
 
   samba = samba4;
@@ -9238,10 +9173,6 @@ with pkgs;
     '';
   };
 
-  nullmailer = callPackage ../servers/mail/nullmailer {
-    stdenv = gccStdenv;
-  };
-
   openmoji-color = callPackage ../data/fonts/openmoji { fontFormats = [ "glyf_colr_0" ]; };
 
   openmoji-black = callPackage ../data/fonts/openmoji { fontFormats = [ "glyf" ]; };