treewide: remove all-packages.nix overrides of packages defined in by-name (A-C) (#469771)

pkgs/by-name/ak/akkoma-admin-fe/package.nix

@@ -4,7 +4,7 @@
   fetchFromGitea,
   yarn-berry_3,
   nodejs,
-  python3,
+  python311,
   pkg-config,
   libsass,
   xcbuild,
@@ -39,7 +39,7 @@ stdenv.mkDerivation (finalAttrs: {
     yarn-berry
     nodejs
     pkg-config
-    python3
+    python311
     libsass
   ]
   ++ lib.optional stdenv.hostPlatform.isDarwin xcbuild;

pkgs/by-name/ak/akkoma/package.nix

@@ -1,6 +1,6 @@
 {
   lib,
-  beamPackages,
+  beam_minimal,
   fetchFromGitea,
   cmake,
   file,
@@ -8,6 +8,16 @@
   nix-update-script,
 }:
 
+let
+  beamPackages = beam_minimal.packages.erlang_26.extend (
+    self: super: {
+      elixir = self.elixir_1_16;
+      rebar3 = self.rebar3WithPlugins {
+        plugins = with self; [ pc ];
+      };
+    }
+  );
+in
 beamPackages.mixRelease rec {
   pname = "akkoma";
   version = "3.17.0";

pkgs/by-name/al/alsa-utils/package.nix

@@ -14,7 +14,7 @@
   procps,
   tree,
   which,
-  fftw,
+  fftwFloat,
   pipewire,
   withPipewireLib ? true,
   symlinkJoin,
@@ -48,7 +48,7 @@ stdenv.mkDerivation (finalAttrs: {
     alsa-lib
     ncurses
     libsamplerate
-    fftw
+    fftwFloat
   ];
 
   configureFlags = [

pkgs/by-name/aq/aquamarine/package.nix

@@ -1,6 +1,6 @@
 {
   lib,
-  stdenv,
+  gcc15Stdenv,
   cmake,
   fetchFromGitHub,
   hwdata,
@@ -21,7 +21,7 @@
   wayland-protocols,
   wayland-scanner,
 }:
-stdenv.mkDerivation (finalAttrs: {
+gcc15Stdenv.mkDerivation (finalAttrs: {
   pname = "aquamarine";
   version = "0.10.0";
 

pkgs/by-name/ar/armips/package.nix

@@ -1,11 +1,11 @@
 {
-  stdenv,
+  clangStdenv,
   lib,
   fetchFromGitHub,
   cmake,
 }:
 
-stdenv.mkDerivation rec {
+clangStdenv.mkDerivation rec {
   pname = "armips";
   version = "0.11.0";
 

pkgs/by-name/ar/art/package.nix

@@ -22,7 +22,7 @@
   lcms2,
   libraw,
   libiptcdata,
-  fftw,
+  fftwSinglePrec,
   expat,
   pcre2,
   libsigcxx,
@@ -81,7 +81,7 @@ stdenv.mkDerivation rec {
     lcms2
     libraw
     libiptcdata
-    fftw
+    fftwSinglePrec
     expat
     pcre2
     libsigcxx

pkgs/by-name/at/atf/package.nix

@@ -1,6 +1,7 @@
 {
   lib,
   stdenv,
+  darwin,
   fetchFromGitHub,
   fetchpatch,
   autoreconfHook,
@@ -8,7 +9,11 @@
   gitUpdater,
 }:
 
-stdenv.mkDerivation (finalAttrs: {
+let
+  # atf is a dependency of libiconv. Avoid an infinite recursion with `pkgsStatic` by using a bootstrap stdenv.
+  stdenv' = if stdenv.hostPlatform.isDarwin then darwin.bootstrapStdenv else stdenv;
+in
+stdenv'.mkDerivation (finalAttrs: {
   pname = "atf";
   version = "0.23";
 
@@ -26,12 +31,12 @@ stdenv.mkDerivation (finalAttrs: {
         --replace-fail 'atf_test_program{name="srcdir_test"}' ""
     ''
     # These tests fail on Darwin.
-    + lib.optionalString (finalAttrs.doInstallCheck && stdenv.hostPlatform.isDarwin) ''
+    + lib.optionalString (finalAttrs.doInstallCheck && stdenv'.hostPlatform.isDarwin) ''
       substituteInPlace atf-c/detail/process_test.c \
         --replace-fail 'ATF_TP_ADD_TC(tp, status_coredump);' ""
     ''
     # This test fails on Linux.
-    + lib.optionalString (finalAttrs.doInstallCheck && stdenv.hostPlatform.isLinux) ''
+    + lib.optionalString (finalAttrs.doInstallCheck && stdenv'.hostPlatform.isLinux) ''
       substituteInPlace atf-c/detail/fs_test.c \
         --replace-fail 'ATF_TP_ADD_TC(tp, eaccess);' ""
     '';

pkgs/by-name/ba/basalt-monado/package.nix

@@ -25,6 +25,10 @@
   cudaPackages,
   enableCuda ? config.cudaSupport,
 }:
+
+let
+  opencv' = opencv.override { enableGtk3 = true; };
+in
 stdenv.mkDerivation {
   pname = "basalt-monado";
   version = "0-unstable-2025-09-25";
@@ -57,7 +61,7 @@ stdenv.mkDerivation {
     libGL
     lz4
     magic-enum
-    opencv.cxxdev
+    opencv'.cxxdev
     onetbb
     xorg.libX11
   ]

pkgs/by-name/ba/bazel_7/package.nix

@@ -12,7 +12,8 @@
   buildFHSEnv,
   # this package (through the fixpoint glass)
   # TODO probably still need for tests at some point
-  bazel_self,
+  bazel_7,
+  bazel_self ? bazel_7,
   # native build inputs
   runtimeShell,
   zip,
@@ -35,10 +36,11 @@
   # Apple dependencies
   cctools,
   libtool,
-  sigtool,
+  darwin,
   # Allow to independently override the jdks used to build and run respectively
-  buildJdk,
-  runJdk,
+  jdk21_headless,
+  buildJdk ? jdk21_headless,
+  runJdk ? jdk21_headless,
   # Toggle for hacks for running bazel under buildBazelPackage:
   # Always assume all markers valid (this is needed because we remove markers; they are non-deterministic).
   # Also, don't clean up environment variables (so that NIX_ environment variables are passed to compilers).
@@ -417,7 +419,7 @@ stdenv.mkDerivation rec {
         # don't use system installed Xcode to run clang, use Nix clang instead
         sed -i -E \
           -e "s;/usr/bin/xcrun (--sdk macosx )?clang;${stdenv.cc}/bin/clang $NIX_CFLAGS_COMPILE $(bazelLinkFlags) -framework CoreFoundation;g" \
-          -e "s;/usr/bin/codesign;CODESIGN_ALLOCATE=${cctools}/bin/${cctools.targetPrefix}codesign_allocate ${sigtool}/bin/codesign;" \
+          -e "s;/usr/bin/codesign;CODESIGN_ALLOCATE=${cctools}/bin/${cctools.targetPrefix}codesign_allocate ${darwin.sigtool}/bin/codesign;" \
           scripts/bootstrap/compile.sh \
           tools/osx/BUILD
 

pkgs/by-name/bi/biblioteca/package.nix

@@ -12,7 +12,7 @@
   gtk4,
   gobject-introspection,
   libadwaita,
-  webkitgtk,
+  webkitgtk_6_0,
   coreutils,
   makeShellWrapper,
   wrapGAppsHook4,
@@ -54,7 +54,7 @@ stdenv.mkDerivation (finalAttrs: {
     gtk4
     gobject-introspection
     libadwaita
-    webkitgtk
+    webkitgtk_6_0
     glib-networking
   ];
 
@@ -64,7 +64,7 @@ stdenv.mkDerivation (finalAttrs: {
       gtk4.devdoc
       glib.devdoc
       libadwaita.devdoc
-      webkitgtk.devdoc
+      webkitgtk_6_0.devdoc
       gobject-introspection.devdoc
     ]
     ++ extraDocsPackage;

pkgs/by-name/bl/blender/package.nix

@@ -67,7 +67,7 @@
   pkg-config,
   potrace,
   pugixml,
-  python3Packages, # must use instead of python3.pkgs, see https://github.com/NixOS/nixpkgs/issues/211340
+  python311Packages, # must use python3Packages instead of python3.pkgs, see https://github.com/NixOS/nixpkgs/issues/211340
   rocmPackages, # comes with a significantly larger closure size
   rubberband,
   runCommand,
@@ -95,8 +95,8 @@ let
     (!stdenv.hostPlatform.isAarch64 && stdenv.hostPlatform.isLinux) || stdenv.hostPlatform.isDarwin;
   vulkanSupport = !stdenv.hostPlatform.isDarwin;
 
-  python3 = python3Packages.python;
-  pyPkgsOpenusd = python3Packages.openusd.override (old: {
+  python3 = python311Packages.python;
+  pyPkgsOpenusd = python311Packages.openusd.override (old: {
     opensubdiv = old.opensubdiv.override { inherit cudaSupport; };
     withOsl = false;
   });
@@ -131,7 +131,7 @@ stdenv'.mkDerivation (finalAttrs: {
       substituteInPlace source/creator/CMakeLists.txt \
         --replace-fail '${"$"}{LIBDIR}/python' \
                   '${python3}' \
-        --replace-fail '${"$"}{LIBDIR}/materialx/' '${python3Packages.materialx}/'
+        --replace-fail '${"$"}{LIBDIR}/materialx/' '${python311Packages.materialx}/'
       substituteInPlace build_files/cmake/platform/platform_apple.cmake \
         --replace-fail '${"$"}{LIBDIR}/brotli/lib/libbrotlicommon-static.a' \
                   '${lib.getLib brotli}/lib/libbrotlicommon.dylib' \
@@ -149,12 +149,12 @@ stdenv'.mkDerivation (finalAttrs: {
   cmakeFlags = [
     "-C../build_files/cmake/config/blender_release.cmake"
 
-    (lib.cmakeFeature "MaterialX_DIR" "${python3Packages.materialx}/lib/cmake/MaterialX")
+    (lib.cmakeFeature "MaterialX_DIR" "${python311Packages.materialx}/lib/cmake/MaterialX")
     (lib.cmakeFeature "PYTHON_INCLUDE_DIR" "${python3}/include/${python3.libPrefix}")
     (lib.cmakeFeature "PYTHON_LIBPATH" "${python3}/lib")
     (lib.cmakeFeature "PYTHON_LIBRARY" "${python3.libPrefix}")
-    (lib.cmakeFeature "PYTHON_NUMPY_INCLUDE_DIRS" "${python3Packages.numpy_1}/${python3.sitePackages}/numpy/core/include")
-    (lib.cmakeFeature "PYTHON_NUMPY_PATH" "${python3Packages.numpy_1}/${python3.sitePackages}")
+    (lib.cmakeFeature "PYTHON_NUMPY_INCLUDE_DIRS" "${python311Packages.numpy_1}/${python3.sitePackages}/numpy/core/include")
+    (lib.cmakeFeature "PYTHON_NUMPY_PATH" "${python311Packages.numpy_1}/${python3.sitePackages}")
     (lib.cmakeFeature "PYTHON_VERSION" "${python3.pythonVersion}")
 
     (lib.cmakeBool "WITH_BUILDINFO" false)
@@ -221,7 +221,7 @@ stdenv'.mkDerivation (finalAttrs: {
     cmake
     llvmPackages.llvm.dev
     makeWrapper
-    python3Packages.wrapPython
+    python311Packages.wrapPython
   ]
   ++ lib.optionals cudaSupport [
     addDriverRunpath
@@ -263,7 +263,7 @@ stdenv'.mkDerivation (finalAttrs: {
     potrace
     pugixml
     python3
-    python3Packages.materialx
+    python311Packages.materialx
     rubberband
     zlib
     zstd
@@ -316,7 +316,7 @@ stdenv'.mkDerivation (finalAttrs: {
 
   pythonPath =
     let
-      ps = python3Packages;
+      ps = python311Packages;
     in
     [
       ps.materialx
@@ -362,13 +362,13 @@ stdenv'.mkDerivation (finalAttrs: {
 
   passthru = {
     python = python3;
-    pythonPackages = python3Packages;
+    pythonPackages = python311Packages;
 
     withPackages =
       f:
       (callPackage ./wrapper.nix { }).override {
         blender = finalAttrs.finalPackage;
-        extraModules = (f python3Packages);
+        extraModules = (f python311Packages);
       };
 
     tests = {

pkgs/by-name/bl/bluespec/package.nix

@@ -17,7 +17,8 @@
   yices, # bsc uses a patched version of yices
   zlib,
   ghc,
-  gmp-static,
+  gmp,
+  gmp-static ? gmp.override { withStatic = true; },
   iverilog,
   asciidoctor,
   texliveFull,

pkgs/by-name/ca/cantata/package.nix

@@ -25,7 +25,7 @@
   withHttpStream ? true,
   gst_all_1,
   withReplaygain ? true,
-  ffmpeg,
+  ffmpeg_6,
   speex,
   mpg123,
   withMtp ? true,
@@ -92,7 +92,7 @@ let
       ];
       enable = withReplaygain;
       pkgs = [
-        ffmpeg
+        ffmpeg_6
         speex
         mpg123
       ];

pkgs/by-name/cl/clang-uml/package.nix

@@ -1,7 +1,7 @@
 {
   lib,
   fetchFromGitHub,
-  stdenv,
+  clangStdenv,
   cmake,
   pkg-config,
   installShellFiles,
@@ -15,7 +15,7 @@
   enableLibcxx ? false,
   debug ? false,
 }:
-stdenv.mkDerivation (finalAttrs: {
+clangStdenv.mkDerivation (finalAttrs: {
   pname = "clang-uml";
   version = "0.6.2";
 

pkgs/by-name/cl/clash-verge-rev/package.nix

@@ -8,7 +8,7 @@
   wrapGAppsHook3,
   v2ray-geoip,
   v2ray-domain-list-community,
-  libsoup,
+  libsoup_3,
 }:
 let
   pname = "clash-verge-rev";
@@ -38,7 +38,7 @@ let
       pnpm-hash
       vendor-hash
       meta
-      libsoup
+      libsoup_3
       ;
   };
 

pkgs/by-name/cl/clash-verge-rev/unwrapped.nix

@@ -23,7 +23,7 @@
   kdePackages,
   libayatana-appindicator,
   libsForQt5,
-  libsoup,
+  libsoup_3,
   openssl,
   webkitgtk_4_1,
 }:
@@ -106,7 +106,7 @@ rustPlatform.buildRustPackage {
 
   buildInputs = [
     libayatana-appindicator
-    libsoup
+    libsoup_3
     openssl
     webkitgtk_4_1
   ];

pkgs/by-name/co/cope/package.nix

@@ -1,10 +1,12 @@
 {
   lib,
   fetchFromGitHub,
-  perl,
-  perlPackages,
+  perl538Packages,
   makeWrapper,
 }:
+let
+  perlPackages = perl538Packages;
+in
 perlPackages.buildPerlPackage {
   pname = "cope";
   version = "0-unstable-2025-06-20";
@@ -50,7 +52,7 @@ perlPackages.buildPerlPackage {
         if [[ -f "$script" && -x "$script" ]]; then
           wrapProgram "$script" \
             --set PERL5LIB "${perlPath}:$out/lib/perl5/site_perl"
-          sed -i "1s|^#!.*perl|#!${perl}/bin/perl|" "$out/libexec/.''${script##*/}-wrapped"
+          sed -i "1s|^#!.*perl|#!${perlPackages.perl}/bin/perl|" "$out/libexec/.''${script##*/}-wrapped"
         fi
       done
       rm -r $out/${perlPackages.perl.libPrefix}/${perlPackages.perl.version}/auto

pkgs/by-name/cp/cp2k/package.nix

@@ -12,7 +12,7 @@
   fftw,
   libint,
   libvori,
-  libxc,
+  libxc_7,
   dftd4,
   simple-dftd3,
   tblite,
@@ -165,7 +165,7 @@ stdenv.mkDerivation rec {
     gsl
     libint
     libvori
-    libxc
+    libxc_7
     libxsmm
     mpi
     spglib

pkgs/top-level/all-packages.nix

@@ -277,10 +277,6 @@ with pkgs;
 
   cve = with python3Packages; toPythonApplication cvelib;
 
-  basalt-monado = callPackage ../by-name/ba/basalt-monado/package.nix {
-    opencv = opencv.override { enableGtk3 = true; };
-  };
-
   bloodhound-py = with python3Packages; toPythonApplication bloodhound-py;
 
   # Zip file format only allows times after year 1980, which makes e.g. Python
@@ -323,15 +319,6 @@ with pkgs;
 
   chef-cli = callPackage ../tools/misc/chef-cli { };
 
-  clang-uml = callPackage ../by-name/cl/clang-uml/package.nix {
-    stdenv = clangStdenv;
-  };
-
-  cope = callPackage ../by-name/co/cope/package.nix {
-    perl = perl538;
-    perlPackages = perl538Packages;
-  };
-
   coolercontrol = recurseIntoAttrs (callPackage ../applications/system/coolercontrol { });
 
   cup-docker-noserver = cup-docker.override { withServer = false; };
@@ -974,21 +961,6 @@ with pkgs;
 
   opnplug = adlplug.override { type = "OPN"; };
 
-  akkoma = callPackage ../by-name/ak/akkoma/package.nix {
-    beamPackages = beam_minimal.packages.erlang_26.extend (
-      self: super: {
-        elixir = self.elixir_1_16;
-        rebar3 = self.rebar3WithPlugins {
-          plugins = with self; [ pc ];
-        };
-      }
-    );
-  };
-
-  akkoma-admin-fe = callPackage ../by-name/ak/akkoma-admin-fe/package.nix {
-    python3 = python311;
-  };
-
   aegisub = callPackage ../by-name/ae/aegisub/package.nix (
     {
       luajit = luajit.override { enable52Compat = true; };
@@ -1968,10 +1940,6 @@ with pkgs;
     cairo = cairo.override { xcbSupport = true; };
   };
 
-  aquamarine = callPackage ../by-name/aq/aquamarine/package.nix {
-    stdenv = gcc15Stdenv;
-  };
-
   hyprshade = python3Packages.callPackage ../applications/window-managers/hyprwm/hyprshade { };
 
   hyprlandPlugins = recurseIntoAttrs (
@@ -4169,19 +4137,11 @@ with pkgs;
   adaptivecppWithCuda = adaptivecpp.override { cudaSupport = true; };
   adaptivecppWithRocm = adaptivecpp.override { rocmSupport = true; };
 
-  armips = callPackage ../by-name/ar/armips/package.nix {
-    stdenv = clangStdenv;
-  };
-
   binaryen = callPackage ../development/compilers/binaryen {
     nodejs = nodejs-slim;
     inherit (python3Packages) filecheck;
   };
 
-  bluespec = callPackage ../by-name/bl/bluespec/package.nix {
-    gmp-static = gmp.override { withStatic = true; };
-  };
-
   codon = callPackage ../development/compilers/codon {
     inherit (llvmPackages) lld stdenv;
   };
@@ -5946,13 +5906,6 @@ with pkgs;
 
   bazel = bazel_7;
 
-  bazel_7 = callPackage ../by-name/ba/bazel_7/package.nix {
-    inherit (darwin) sigtool;
-    buildJdk = jdk21_headless;
-    runJdk = jdk21_headless;
-    bazel_self = bazel_7;
-  };
-
   buildifier = bazel-buildtools;
   buildozer = bazel-buildtools;
   unused_deps = bazel-buildtools;
@@ -8558,12 +8511,6 @@ with pkgs;
 
   ### DEVELOPMENT / TESTING TOOLS
 
-  atf = callPackage ../by-name/at/atf/package.nix {
-    stdenv =
-      # atf is a dependency of libiconv. Avoid an infinite recursion with `pkgsStatic` by using a bootstrap stdenv.
-      if stdenv.hostPlatform.isDarwin then darwin.bootstrapStdenv else stdenv;
-  };
-
   ### DEVELOPMENT / LIBRARIES / AGDA
 
   agdaPackages = recurseIntoAttrs (
@@ -9564,10 +9511,6 @@ with pkgs;
 
   alfred = callPackage ../os-specific/linux/batman-adv/alfred.nix { };
 
-  alsa-utils = callPackage ../by-name/al/alsa-utils/package.nix {
-    fftw = fftwFloat;
-  };
-
   arm-trusted-firmware = callPackage ../misc/arm-trusted-firmware { };
   inherit (arm-trusted-firmware)
     buildArmTrustedFirmware
@@ -10427,10 +10370,6 @@ with pkgs;
     pinentry = pinentry-curses;
   };
 
-  blender = callPackage ../by-name/bl/blender/package.nix {
-    python3Packages = python311Packages;
-  };
-
   blender-hip = blender.override { hipSupport = true; };
 
   blucontrol = callPackage ../applications/misc/blucontrol/wrapper.nix {
@@ -12626,10 +12565,6 @@ with pkgs;
   anki-utils = callPackage ../by-name/an/anki/addons/anki-utils.nix { };
   ankiAddons = recurseIntoAttrs (callPackage ../by-name/an/anki/addons { });
 
-  art = callPackage ../by-name/ar/art/package.nix {
-    fftw = fftwSinglePrec;
-  };
-
   arx-libertatis = libsForQt5.callPackage ../games/arx-libertatis { };
 
   beancount-ing-diba = callPackage ../applications/office/beancount/beancount-ing-diba.nix {
@@ -13105,10 +13040,6 @@ with pkgs;
 
   siesta-mpi = callPackage ../applications/science/chemistry/siesta { useMpi = true; };
 
-  cp2k = callPackage ../by-name/cp/cp2k/package.nix {
-    libxc = pkgs.libxc_7;
-  };
-
   ### SCIENCE/BIOLOGY
 
   cd-hit = callPackage ../applications/science/biology/cd-hit {
@@ -14125,26 +14056,14 @@ with pkgs;
     fltk = fltk13;
   };
 
-  cantata = callPackage ../by-name/ca/cantata/package.nix {
-    ffmpeg = ffmpeg_6;
-  };
-
   libkazv = callPackage ../by-name/li/libkazv/package.nix {
     libcpr = libcpr_1_10_5;
   };
 
-  biblioteca = callPackage ../by-name/bi/biblioteca/package.nix {
-    webkitgtk = webkitgtk_6_0;
-  };
-
   libpostalWithData = callPackage ../by-name/li/libpostal/package.nix {
     withData = true;
   };
 
-  clash-verge-rev = callPackage ../by-name/cl/clash-verge-rev/package.nix {
-    libsoup = libsoup_3;
-  };
-
   gpac-unstable = callPackage ../by-name/gp/gpac/package.nix {
     releaseChannel = "unstable";
   };