treewide: migrate to pkgs/by-name

All from https://github.com/Aleksanaa/by-name-migrate, with some additional
exclusions of packages with open PRs to prevent merge conflicts.

pkgs/top-level/all-packages.nix

@@ -2160,8 +2160,6 @@ with pkgs;
 
   easyocr = with python3.pkgs; toPythonApplication easyocr;
 
-  eddy = callPackage ../applications/graphics/eddy { };
-
   element-web = callPackage ../by-name/el/element-web/package.nix {
     conf = config.element-web.conf or { };
   };
@@ -2999,8 +2997,6 @@ with pkgs;
     inherit (darwin) autoSignDarwinBinariesHook;
   };
 
-  fontmatrix = callPackage ../applications/graphics/fontmatrix { };
-
   fox = callPackage ../development/libraries/fox { };
 
   fox_1_6 = callPackage ../development/libraries/fox/fox-1.6.nix { };
@@ -3021,10 +3017,6 @@ with pkgs;
 
   frostwire-bin = callPackage ../applications/networking/p2p/frostwire/frostwire-bin.nix { };
 
-  fstl = callPackage ../applications/graphics/fstl { };
-
-  fwknop = callPackage ../tools/security/fwknop { };
-
   uniscribe = callPackage ../tools/text/uniscribe { };
 
   gandi-cli = python3Packages.callPackage ../tools/networking/gandi-cli { };
@@ -3488,8 +3480,6 @@ with pkgs;
 
   ksmoothdock = libsForQt5.callPackage ../applications/misc/ksmoothdock { };
 
-  leocad = callPackage ../applications/graphics/leocad { };
-
   libcoap = callPackage ../applications/networking/libcoap {
     autoconf = buildPackages.autoconf269;
   };
@@ -3954,8 +3944,6 @@ with pkgs;
     jre = pkgs.jre_headless;
   };
 
-  openboard = callPackage ../applications/graphics/openboard { };
-
   ophcrack-cli = ophcrack.override { enableGui = false; };
 
   open-interpreter = with python3Packages; toPythonApplication open-interpreter;
@@ -4061,8 +4049,6 @@ with pkgs;
 
   ossec-server = callPackage ../tools/security/ossec/server.nix { };
 
-  ovito = callPackage ../applications/graphics/ovito { };
-
   p4c = callPackage ../development/compilers/p4c {
     protobuf = protobuf_21;
   };
@@ -4270,20 +4256,12 @@ with pkgs;
 
   qmarkdowntextedit = libsForQt5.callPackage ../development/libraries/qmarkdowntextedit { };
 
-  qosmic = callPackage ../applications/graphics/qosmic { };
-
-  qtikz = callPackage ../applications/graphics/ktikz { };
-
   qtspim = libsForQt5.callPackage ../development/tools/misc/qtspim { };
 
   quictls = callPackage ../development/libraries/quictls { };
 
   quota = if stdenv.hostPlatform.isLinux then linuxquota else unixtools.quota;
 
-  qvge = callPackage ../applications/graphics/qvge { };
-
-  qview = callPackage ../applications/graphics/qview { };
-
   wayback_machine_downloader = callPackage ../applications/networking/wayback_machine_downloader { };
 
   radeon-profile = libsForQt5.callPackage ../tools/misc/radeon-profile { };
@@ -4438,8 +4416,6 @@ with pkgs;
 
   soundkonverter = libsForQt5.soundkonverter;
 
-  sparrow = callPackage ../applications/blockchains/sparrow { };
-
   steck = callPackage ../servers/pinnwand/steck.nix { };
 
   stm32loader = with python3Packages; toPythonApplication stm32loader;
@@ -7163,8 +7139,6 @@ with pkgs;
 
   chruby = callPackage ../development/tools/misc/chruby { rubies = null; };
 
-  cloudcompare = callPackage ../applications/graphics/cloudcompare { };
-
   cookiecutter = with python3Packages; toPythonApplication cookiecutter;
 
   corundum = callPackage ../development/tools/corundum { };
@@ -7245,8 +7219,6 @@ with pkgs;
     else
       gcc.cc;
 
-  libsigrok = callPackage ../development/tools/libsigrok { };
-
   distcc = callPackage ../development/tools/misc/distcc {
     libiberty_static = libiberty.override { staticBuild = true; };
   };
@@ -7357,8 +7329,6 @@ with pkgs;
   gradle_8 = wrapGradle gradle_8-unwrapped null;
   gradle = wrapGradle gradle-unwrapped "gradle-unwrapped";
 
-  gperf = callPackage ../development/tools/misc/gperf { };
-
   griffe = with python3Packages; toPythonApplication griffe;
 
   gwrap = g-wrap;
@@ -8130,8 +8100,6 @@ with pkgs;
     inherit (darwin) DarwinTools;
   };
 
-  givaro = callPackage ../development/libraries/givaro { };
-
   ghp-import = with python3Packages; toPythonApplication ghp-import;
 
   ghcid = haskellPackages.ghcid.bin;
@@ -8357,8 +8325,6 @@ with pkgs;
 
   cairomm_1_16 = callPackage ../development/libraries/cairomm/1.16.nix { };
 
-  pango = callPackage ../development/libraries/pango { };
-
   pangomm = callPackage ../development/libraries/pangomm { };
 
   pangomm_2_48 = callPackage ../development/libraries/pangomm/2.48.nix { };
@@ -8639,8 +8605,6 @@ with pkgs;
 
   libchipcard = callPackage ../development/libraries/aqbanking/libchipcard.nix { };
 
-  libcomps = callPackage ../tools/package-management/libcomps { };
-
   libcxxrt = callPackage ../development/libraries/libcxxrt {
     stdenv =
       if stdenv.hostPlatform.useLLVM or false then
@@ -8663,8 +8627,6 @@ with pkgs;
     withXorg = false;
   };
 
-  libdnf = callPackage ../tools/package-management/libdnf { };
-
   libdvdnav = callPackage ../development/libraries/libdvdnav { };
   libdvdnav_4_2_1 = callPackage ../development/libraries/libdvdnav/4.2.1.nix {
     libdvdread = libdvdread_4_9_9;
@@ -8688,8 +8650,6 @@ with pkgs;
     callPackage ../development/libraries/libgnome-games-support/2.0.nix
       { };
 
-  libiio = callPackage ../development/libraries/libiio { };
-
   libextractor = callPackage ../development/libraries/libextractor {
     libmpeg2 = mpeg2dec;
   };
@@ -8854,8 +8814,6 @@ with pkgs;
     protobuf = protobuf_21;
   };
 
-  libpwquality = callPackage ../development/libraries/libpwquality { };
-
   libsigcxx = callPackage ../development/libraries/libsigcxx { };
 
   libsigcxx30 = callPackage ../development/libraries/libsigcxx/3.0.nix { };
@@ -9184,8 +9142,6 @@ with pkgs;
     };
   };
 
-  opencsg = callPackage ../development/libraries/opencsg { };
-
   opencv4 = callPackage ../development/libraries/opencv/4.x.nix {
     pythonPackages = python3Packages;
     # TODO: LTO does not work.
@@ -9221,8 +9177,6 @@ with pkgs;
   watcherclient = with python312Packages; toPythonApplication python-watcherclient;
   zunclient = with python312Packages; toPythonApplication python-zunclient;
 
-  openvdb = callPackage ../development/libraries/openvdb { };
-
   inherit (callPackages ../development/libraries/libressl { })
     libressl_3_6
     libressl_3_7
@@ -9663,8 +9617,6 @@ with pkgs;
 
   structuresynth = libsForQt5.callPackage ../development/libraries/structuresynth { };
 
-  sundials = callPackage ../development/libraries/sundials { };
-
   svxlink = libsForQt5.callPackage ../applications/radio/svxlink { };
 
   szurubooru = callPackage ../servers/web-apps/szurubooru { };
@@ -10316,8 +10268,6 @@ with pkgs;
   freshrss = callPackage ../servers/web-apps/freshrss { };
   freshrss-extensions = recurseIntoAttrs (callPackage ../servers/web-apps/freshrss/extensions { });
 
-  glabels-qt = callPackage ../applications/graphics/glabels-qt { };
-
   grafana = callPackage ../servers/monitoring/grafana { };
   grafanaPlugins = callPackages ../servers/monitoring/grafana/plugins { };
 
@@ -12011,10 +11961,6 @@ with pkgs;
 
   cdparanoia = cdparanoiaIII;
 
-  brotab = callPackage ../tools/misc/brotab { };
-
-  bumblebee-status = callPackage ../applications/window-managers/i3/bumblebee-status { };
-
   chromium = callPackage ../applications/networking/browsers/chromium (config.chromium or { });
 
   chuck = callPackage ../applications/audio/chuck {
@@ -12138,7 +12084,6 @@ with pkgs;
   };
   drawio-headless = callPackage ../applications/graphics/drawio/headless.nix { };
 
-  drawpile = callPackage ../applications/graphics/drawpile { };
   drawpile-server-headless = drawpile.override {
     buildClient = false;
     buildServerGui = false;
@@ -12208,8 +12153,6 @@ with pkgs;
 
   espeakedit = callPackage ../applications/audio/espeak/edit.nix { };
 
-  evilpixie = callPackage ../applications/graphics/evilpixie { };
-
   greenfoot = callPackage ../applications/editors/greenfoot {
     openjdk = openjdk21.override {
       enableJavaFX = true;
@@ -12219,8 +12162,6 @@ with pkgs;
 
   haruna = kdePackages.callPackage ../applications/video/haruna { };
 
-  hdrmerge = callPackage ../applications/graphics/hdrmerge { };
-
   input-leap = qt6Packages.callPackage ../applications/misc/input-leap {
     avahi = avahi.override { withLibdnssdCompat = true; };
   };
@@ -12679,8 +12620,6 @@ with pkgs;
 
   pixel2svg = python310Packages.callPackage ../tools/graphics/pixel2svg { };
 
-  pixinsight = callPackage ../applications/graphics/pixinsight { };
-
   inherit (callPackage ../applications/virtualization/singularity/packages.nix { })
     apptainer
     singularity
@@ -12783,8 +12722,6 @@ with pkgs;
     subversionSupport = true;
   };
 
-  iksemel = callPackage ../development/libraries/iksemel { };
-
   avalonia-ilspy = callPackage ../applications/misc/avalonia-ilspy {
     inherit (darwin) autoSignDarwinBinariesHook;
   };
@@ -12858,8 +12795,6 @@ with pkgs;
 
   img2pdf = with python3Packages; toPythonApplication img2pdf;
 
-  imgp = callPackage ../applications/graphics/imgp { };
-
   inkscape = callPackage ../applications/graphics/inkscape {
     lcms = lcms2;
   };
@@ -12927,8 +12862,6 @@ with pkgs;
 
   kexi = libsForQt5.callPackage ../applications/office/kexi { };
 
-  kgraphviewer = callPackage ../applications/graphics/kgraphviewer { };
-
   kid3-cli = kid3.override {
     withCLI = true;
     withKDE = false;
@@ -13193,9 +13126,6 @@ with pkgs;
 
   meshcentral = callPackage ../tools/admin/meshcentral { };
 
-  meshlab = callPackage ../applications/graphics/meshlab { };
-  meshlab-unstable = callPackage ../applications/graphics/meshlab-unstable { };
-
   michabo = libsForQt5.callPackage ../applications/misc/michabo { };
 
   miniaudicle = qt6Packages.callPackage ../applications/audio/miniaudicle { };
@@ -13297,8 +13227,6 @@ with pkgs;
 
   rquickshare-legacy = rquickshare.override { app-type = "legacy"; };
 
-  seamly2d = callPackage ../applications/graphics/seamly2d { };
-
   # a somewhat more maintained fork of ympd
   memento = qt6Packages.callPackage ../applications/video/memento { };
 
@@ -13507,10 +13435,6 @@ with pkgs;
     kreative-square
     ;
 
-  openscad = callPackage ../applications/graphics/openscad { };
-
-  opentoonz = callPackage ../applications/graphics/opentoonz { };
-
   opentx = libsForQt5.callPackage ../applications/misc/opentx { };
 
   organicmaps = qt6Packages.callPackage ../applications/misc/organicmaps { };
@@ -13564,10 +13488,6 @@ with pkgs;
     stdenv = gccStdenv;
   };
 
-  photoflare = callPackage ../applications/graphics/photoflare { };
-
-  phototonic = callPackage ../applications/graphics/phototonic { };
-
   pianobooster = qt5.callPackage ../applications/audio/pianobooster { };
 
   pianoteq = callPackage ../applications/audio/pianoteq { };
@@ -13635,8 +13555,6 @@ with pkgs;
 
   qcad = libsForQt5.callPackage ../applications/misc/qcad { };
 
-  qcomicbook = callPackage ../applications/graphics/qcomicbook { };
-
   qctools = libsForQt5.callPackage ../applications/video/qctools { };
 
   qelectrotech = libsForQt5.callPackage ../applications/misc/qelectrotech { };
@@ -13669,8 +13587,6 @@ with pkgs;
 
   qjackctl = libsForQt5.callPackage ../applications/audio/qjackctl { };
 
-  qimgv = callPackage ../applications/graphics/qimgv { };
-
   qmediathekview = libsForQt5.callPackage ../applications/video/qmediathekview { };
 
   qmplay2-qt5 = qmplay2.override { qtVersion = "5"; };
@@ -13684,8 +13600,6 @@ with pkgs;
 
   qsampler = libsForQt5.callPackage ../applications/audio/qsampler { };
 
-  qscreenshot = callPackage ../applications/graphics/qscreenshot { };
-
   qsstv = qt5.callPackage ../applications/radio/qsstv { };
 
   qsyncthingtray = libsForQt5.callPackage ../applications/misc/qsyncthingtray { };
@@ -13769,8 +13683,6 @@ with pkgs;
     wxGTK = wxGTK32;
   };
 
-  rapid-photo-downloader = callPackage ../applications/graphics/rapid-photo-downloader { };
-
   rawtherapee = callPackage ../applications/graphics/rawtherapee {
     fftw = fftwSinglePrec;
   };
@@ -13926,8 +13838,6 @@ with pkgs;
 
   skrooge = libsForQt5.callPackage ../applications/office/skrooge { };
 
-  smartdeblur = callPackage ../applications/graphics/smartdeblur { };
-
   soci = callPackage ../development/libraries/soci { };
 
   socialscan = with python3.pkgs; toPythonApplication socialscan;
@@ -14352,8 +14262,6 @@ with pkgs;
     vscode-generic = ../applications/editors/vscode/generic.nix;
   };
 
-  openvscode-server = callPackage ../servers/openvscode-server { };
-
   code-server = callPackage ../servers/code-server {
     nodejs = nodejs_20;
   };
@@ -14999,8 +14907,6 @@ with pkgs;
   luanti-client = luanti.override { buildServer = false; };
   luanti-server = luanti.override { buildClient = false; };
 
-  mnemosyne = callPackage ../games/mnemosyne { };
-
   mrrescue = callPackage ../games/mrrescue { love = love_0_10; };
 
   mudlet = libsForQt5.callPackage ../games/mudlet {
@@ -15431,8 +15337,6 @@ with pkgs;
 
   deepdiff = with python3Packages; toPythonApplication deepdiff;
 
-  deepsecrets = callPackage ../tools/security/deepsecrets { };
-
   deep-translator = with python3Packages; toPythonApplication deep-translator;
 
   hh-suite = callPackage ../applications/science/biology/hh-suite {
@@ -15456,8 +15360,6 @@ with pkgs;
     useRx3d = true;
   };
 
-  mrtrix = callPackage ../applications/science/biology/mrtrix { };
-
   minc_tools = callPackage ../applications/science/biology/minc-tools {
     inherit (perlPackages) perl TextFormat;
   };
@@ -15466,8 +15368,6 @@ with pkgs;
 
   raxml-mpi = raxml.override { useMpi = true; };
 
-  samtools = callPackage ../applications/science/biology/samtools { };
-
   trimmomatic = callPackage ../applications/science/biology/trimmomatic {
     jdk = pkgs.jdk21_headless;
     # Reduce closure size
@@ -15956,8 +15856,6 @@ with pkgs;
     inherit (ocaml-ng.ocamlPackages_4_14) ocaml;
   };
 
-  ns-3 = callPackage ../development/libraries/science/networking/ns-3 { };
-
   spyder = with python3.pkgs; toPythonApplication spyder;
 
   stellarium = qt6Packages.callPackage ../applications/science/astronomy/stellarium { };
@@ -15974,8 +15872,6 @@ with pkgs;
     python = null;
   };
 
-  lhapdf = callPackage ../development/libraries/physics/lhapdf { };
-
   pythia = callPackage ../development/libraries/physics/pythia {
     hepmc = hepmc2;
   };
@@ -16394,8 +16290,6 @@ with pkgs;
 
   qtrvsim = libsForQt5.callPackage ../applications/science/computer-architecture/qtrvsim { };
 
-  pick-colour-picker = callPackage ../applications/graphics/pick-colour-picker { };
-
   romdirfs = callPackage ../tools/filesystems/romdirfs {
     stdenv = gccStdenv;
   };
@@ -16576,8 +16470,6 @@ with pkgs;
     SDL_ttf = SDL_ttf.override { SDL = SDL_sixel; };
   };
 
-  yacreader = callPackage ../applications/graphics/yacreader { };
-
   yamale = with python3Packages; toPythonApplication yamale;
 
   zap-chip-gui = zap-chip.override { withGui = true; };