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-rw-r--r--pkgs/top-level/all-packages.nix116
-rw-r--r--pkgs/top-level/darwin-packages.nix36
-rw-r--r--pkgs/top-level/java-packages.nix2
-rw-r--r--pkgs/top-level/perl-packages.nix9
-rw-r--r--pkgs/top-level/python-aliases.nix1
-rw-r--r--pkgs/top-level/python-packages.nix26
-rw-r--r--pkgs/top-level/stage.nix2
7 files changed, 115 insertions, 77 deletions
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 265e588aaaced..9c46a54b464ac 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -1363,7 +1363,7 @@ with pkgs;
 
   fixDarwinDylibNames = makeSetupHook {
     name = "fix-darwin-dylib-names-hook";
-    substitutions = { inherit (binutils) targetPrefix; };
+    substitutions = { inherit (darwin.binutils) targetPrefix; };
     meta.platforms = lib.platforms.darwin;
   } ../build-support/setup-hooks/fix-darwin-dylib-names.sh;
 
@@ -2854,7 +2854,7 @@ with pkgs;
   x16-run = x16.run;
 
   yabause = libsForQt5.callPackage ../applications/emulators/yabause {
-    freeglut = null;
+    libglut = null;
     openal = null;
   };
 
@@ -7789,8 +7789,6 @@ with pkgs;
 
   expliot = callPackage ../tools/security/expliot { };
 
-  f2fs-tools = callPackage ../tools/filesystems/f2fs-tools { };
-
   Fabric = with python3Packages; toPythonApplication fabric;
 
   fail2ban = callPackage ../tools/security/fail2ban { };
@@ -8022,9 +8020,7 @@ with pkgs;
 
   fortune = callPackage ../tools/misc/fortune { };
 
-  fox = callPackage ../development/libraries/fox {
-    inherit (darwin.apple_sdk.frameworks) CoreServices;
-  };
+  fox = callPackage ../development/libraries/fox {};
 
   fox_1_6 = callPackage ../development/libraries/fox/fox-1.6.nix {
     inherit (darwin.apple_sdk.frameworks) CoreServices;
@@ -14640,20 +14636,6 @@ with pkgs;
 
   xvfb-run = callPackage ../tools/misc/xvfb-run {
     inherit (texFunctions) fontsConf;
-
-    # xvfb-run is used by a bunch of things to run tests
-    # and doesn't support hardware accelerated rendering
-    # so remove it from the rebuild heavy path for mesa
-    xorgserver = xorg.xorgserver.overrideAttrs(old: {
-      buildInputs = lib.filter (pkg: lib.getName pkg != "mesa") old.buildInputs;
-      configureFlags = old.configureFlags ++ [
-        "--disable-glamor"
-        "--disable-glx"
-        "--disable-dri"
-        "--disable-dri2"
-        "--disable-dri3"
-      ];
-    });
   };
 
   xvkbd = callPackage ../tools/X11/xvkbd { };
@@ -14971,6 +14953,9 @@ with pkgs;
 
   ### DEVELOPMENT / COMPILERS
 
+  temurin-bin-22 = javaPackages.compiler.temurin-bin.jdk-22;
+  temurin-jre-bin-22 = javaPackages.compiler.temurin-bin.jre-22;
+
   temurin-bin-21 = javaPackages.compiler.temurin-bin.jdk-21;
   temurin-jre-bin-21 = javaPackages.compiler.temurin-bin.jre-21;
 
@@ -14992,8 +14977,8 @@ with pkgs;
   temurin-bin-8 = javaPackages.compiler.temurin-bin.jdk-8;
   temurin-jre-bin-8 = javaPackages.compiler.temurin-bin.jre-8;
 
-  temurin-bin = temurin-bin-21;
-  temurin-jre-bin = temurin-jre-bin-21;
+  temurin-bin = temurin-bin-22;
+  temurin-jre-bin = temurin-jre-bin-22;
 
   semeru-bin-21 = javaPackages.compiler.semeru-bin.jdk-21;
   semeru-jre-bin-21 = javaPackages.compiler.semeru-bin.jre-21;
@@ -17295,11 +17280,11 @@ with pkgs;
   # available as `pythonPackages.tkinter` and can be used as any other Python package.
   # When switching these sets, please update docs at ../../doc/languages-frameworks/python.md
   python2 = python27;
-  python3 = python311;
+  python3 = python312;
 
   # pythonPackages further below, but assigned here because they need to be in sync
   python2Packages = dontRecurseIntoAttrs python27Packages;
-  python3Packages = dontRecurseIntoAttrs python311Packages;
+  python3Packages = dontRecurseIntoAttrs python312Packages;
 
   pypy = pypy2;
   pypy2 = pypy27;
@@ -20015,7 +20000,7 @@ with pkgs;
 
   bicpl = callPackage ../development/libraries/science/biology/bicpl { };
 
-  bicgl = callPackage ../development/libraries/science/biology/bicgl { inherit (darwin.apple_sdk.frameworks) GLUT; };
+  bicgl = callPackage ../development/libraries/science/biology/bicgl { };
 
   # TODO(@Ericson2314): Build bionic libc from source
   bionic = if stdenv.hostPlatform.useAndroidPrebuilt
@@ -20452,7 +20437,9 @@ with pkgs;
   # TODO: Fix references and add justStaticExecutables https://github.com/NixOS/nixpkgs/issues/318013
   emanote = haskellPackages.emanote;
 
-  enchant2 = callPackage ../development/libraries/enchant/2.x.nix { };
+  enchant2 = callPackage ../development/libraries/enchant/2.x.nix {
+    inherit (darwin.apple_sdk.frameworks) Cocoa;
+  };
   enchant = enchant2;
 
   enet = callPackage ../development/libraries/enet { };
@@ -20563,8 +20550,6 @@ with pkgs;
 
   flint3 = callPackage ../development/libraries/flint/3.nix { };
 
-  flite = callPackage ../development/libraries/flite { };
-
   fltk13 = callPackage ../development/libraries/fltk {
     inherit (darwin.apple_sdk.frameworks) ApplicationServices Carbon Cocoa OpenGL;
   };
@@ -21326,7 +21311,7 @@ with pkgs;
     icu74
   ;
 
-  icu = icu73;
+  icu = icu74;
 
   id3lib = callPackage ../development/libraries/id3lib { };
 
@@ -23140,26 +23125,59 @@ with pkgs;
 
   ## libGL/libGLU/Mesa stuff
 
-  # Default libGL implementation, should provide headers and
-  # libGL.so/libEGL.so/... to link agains them. Android NDK provides
-  # an OpenGL implementation, we can just use that.
-  libGL = if stdenv.hostPlatform.useAndroidPrebuilt then stdenv
-          else callPackage ../development/libraries/mesa/stubs.nix {
-            inherit (darwin.apple_sdk.frameworks) OpenGL;
-          };
+  # Default libGL implementation.
+  #
+  # Android NDK provides an OpenGL implementation, we can just use that.
+  #
+  # On macOS, we use the OpenGL framework. Packages that still need GLX
+  # specifically can pull in libGLX instead. If you have a package that
+  # should work without X11 but it can’t find the library, it may help
+  # to add the path to `NIX_CFLAGS_COMPILE`:
+  #
+  #     -L${libGL}/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
+  #
+  # If you still can’t get it working, please don’t hesitate to ping
+  # @NixOS/darwin-maintainers to ask an expert to take a look.
+  libGL =
+    if stdenv.hostPlatform.useAndroidPrebuilt then
+      stdenv
+    else if stdenv.hostPlatform.isDarwin then
+      darwin.apple_sdk.frameworks.OpenGL
+    else
+      libglvnd;
 
-  # Default libGLU
-  libGLU = mesa_glu;
+  # On macOS, we use the OpenGL framework. Packages that use libGLX on
+  # macOS may need to depend on mesa_glu directly if this doesn’t work.
+  libGLU =
+    if stdenv.hostPlatform.isDarwin then
+      darwin.apple_sdk.frameworks.OpenGL
+    else
+      mesa_glu;
+
+  # libglvnd does not work (yet?) on macOS.
+  libGLX =
+    if stdenv.hostPlatform.isDarwin then
+      mesa
+    else
+      libglvnd;
+
+  # On macOS, we use the GLUT framework. Packages that use libGLX on
+  # macOS may need to depend on freeglut directly if this doesn’t work.
+  libglut =
+    if stdenv.hostPlatform.isDarwin then
+      darwin.apple_sdk.frameworks.GLUT
+    else
+      freeglut;
+
+  mesa = if stdenv.isDarwin
+    then darwin.apple_sdk_11_0.callPackage ../development/libraries/mesa/darwin.nix {
+      inherit (darwin.apple_sdk_11_0.libs) Xplugin;
+    }
+    else callPackage ../development/libraries/mesa {};
 
-  mesa = darwin.apple_sdk_11_0.callPackage ../development/libraries/mesa {
-    inherit (darwin.apple_sdk_11_0.frameworks) OpenGL;
-    inherit (darwin.apple_sdk_11_0.libs) Xplugin;
-  };
   mesa_i686 = pkgsi686Linux.mesa; # make it build on Hydra
 
-  mesa_glu =  callPackage ../development/libraries/mesa-glu {
-    inherit (darwin.apple_sdk.frameworks) ApplicationServices;
-  };
+  mesa_glu = callPackage ../development/libraries/mesa-glu {};
 
   ## End libGL/libGLU/Mesa stuff
 
@@ -24813,8 +24831,6 @@ with pkgs;
 
   xlslib = callPackage ../development/libraries/xlslib { };
 
-  xsimd = callPackage ../development/libraries/xsimd { };
-
   xtensor = callPackage ../development/libraries/xtensor { };
 
   xtl = callPackage ../development/libraries/xtl { };
@@ -36343,11 +36359,11 @@ with pkgs;
   construoBase = lowPrio (callPackage ../games/construo {
     libGL = null;
     libGLU = null;
-    freeglut = null;
+    libglut = null;
   });
 
   construo = construoBase.override {
-    inherit libGL libGLU freeglut;
+    inherit libGL libGLU libglut;
   };
 
   crack_attack = callPackage ../games/crack-attack { };
diff --git a/pkgs/top-level/darwin-packages.nix b/pkgs/top-level/darwin-packages.nix
index cca74e047dbdd..69d22c8b9625e 100644
--- a/pkgs/top-level/darwin-packages.nix
+++ b/pkgs/top-level/darwin-packages.nix
@@ -83,8 +83,8 @@ impure-cmds // appleSourcePackages // chooseLibs // {
   };
 
   binutils-unwrapped = callPackage ../os-specific/darwin/binutils {
-    inherit (pkgs) binutils-unwrapped;
-    inherit (pkgs.llvmPackages) llvm clang-unwrapped;
+    inherit (self) cctools;
+    inherit (pkgs.llvmPackages) clang-unwrapped llvm llvm-manpages;
   };
 
   binutils = pkgs.wrapBintoolsWith {
@@ -95,17 +95,29 @@ impure-cmds // appleSourcePackages // chooseLibs // {
     bintools = self.binutils-unwrapped;
   };
 
-  binutilsDualAs-unwrapped = callPackage ../os-specific/darwin/binutils {
-    inherit (pkgs) binutils-unwrapped;
-    inherit (pkgs.llvmPackages) llvm clang-unwrapped;
-    dualAs = true;
+  # x86-64 Darwin gnat-bootstrap emits assembly
+  # with MOVQ as the mnemonic for quadword interunit moves
+  # such as `movq %rbp, %xmm0`.
+  # The clang integrated assembler recognises this as valid,
+  # but unfortunately the cctools.gas GNU assembler does not;
+  # it instead uses MOVD as the mnemonic.
+  # The assembly that a GCC build emits is determined at build time
+  # and cannot be changed afterwards.
+  #
+  # To build GNAT on x86-64 Darwin, therefore,
+  # we need both the clang _and_ the cctools.gas assemblers to be available:
+  # the former to build at least the stage1 compiler,
+  # and the latter at least to be detectable
+  # as the target for the final compiler.
+  binutilsDualAs-unwrapped = pkgs.buildEnv {
+    name = "${lib.getName self.binutils-unwrapped}-dualas-${lib.getVersion self.binutils-unwrapped}";
+    paths = [
+      self.binutils-unwrapped
+      (lib.getOutput "gas" self.cctools)
+    ];
   };
 
-  binutilsDualAs = pkgs.wrapBintoolsWith {
-    libc =
-      if stdenv.targetPlatform != stdenv.hostPlatform
-      then pkgs.libcCross
-      else pkgs.stdenv.cc.libc;
+  binutilsDualAs = self.binutils.override {
     bintools = self.binutilsDualAs-unwrapped;
   };
 
@@ -114,7 +126,7 @@ impure-cmds // appleSourcePackages // chooseLibs // {
     bintools = self.binutils-unwrapped;
   };
 
-  cctools = self.cctools-llvm;
+  cctools = self.cctools-port;
 
   cctools-apple = callPackage ../os-specific/darwin/cctools/apple.nix {
     stdenv = if stdenv.isDarwin then stdenv else pkgs.libcxxStdenv;
diff --git a/pkgs/top-level/java-packages.nix b/pkgs/top-level/java-packages.nix
index 2d59c358863b2..c80d6c28f840f 100644
--- a/pkgs/top-level/java-packages.nix
+++ b/pkgs/top-level/java-packages.nix
@@ -227,7 +227,7 @@ in {
       ../development/compilers/openjdk/22.nix
       ../development/compilers/zulu/22.nix
       {
-        openjdk22-bootstrap = temurin-bin.jdk-21;
+        openjdk22-bootstrap = temurin-bin.jdk-22;
         openjfx = openjfx22;
       };
 
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index c2f17f4557ee0..89963580cf742 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -19640,7 +19640,7 @@ with self; {
     };
 
     # FIXME: try with libGL + libGLU instead of libGLU libGL
-    buildInputs = [ pkgs.libGLU pkgs.libGL pkgs.libGLU pkgs.freeglut pkgs.xorg.libX11 pkgs.xorg.libXi pkgs.xorg.libXmu pkgs.xorg.libXext pkgs.xdummy ];
+    buildInputs = [ pkgs.libGLU pkgs.libGL pkgs.libGLU pkgs.libglut pkgs.xorg.libX11 pkgs.xorg.libXi pkgs.xorg.libXmu pkgs.xorg.libXext pkgs.xdummy ];
 
     patches = [ ../development/perl-modules/perl-opengl.patch ];
 
@@ -20344,10 +20344,11 @@ with self; {
         --replace 'WITH_PROJ => undef' 'WITH_PROJ => 0'
     '';
 
-    nativeBuildInputs = with pkgs; [ autoPatchelfHook libGL.dev glibc.dev mesa_glu.dev ];
+    # FIXME: Why are these libraries in `nativeBuildInputs`?
+    nativeBuildInputs = with pkgs; [ autoPatchelfHook (lib.getDev libGL) (lib.getDev glibc) (lib.getDev mesa_glu) ];
 
     buildInputs = [ DevelChecklib TestDeep TestException TestWarn ] ++
-                  (with pkgs; [ gsl freeglut xorg.libXmu xorg.libXi ]);
+                  (with pkgs; [ gsl libglut xorg.libXmu xorg.libXi ]);
 
     propagatedBuildInputs = [
       AstroFITSHeader
@@ -20368,7 +20369,7 @@ with self; {
       homepage = "https://pdl.perl.org";
       license = with lib.licenses; [ artistic1 gpl1Plus ];
       mainProgram = "pdl2";
-      platforms = lib.platforms.linux;
+      platforms = lib.platforms.unix;
     };
   };
 
diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix
index a10f40d615f62..04cc25fb91dbe 100644
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -421,6 +421,7 @@ mapAliases ({
   pytest_6 = pytest; # added 2022-02-10
   pytestcov = pytest-cov; # added 2021-01-04
   pytest-ordering = throw "pytest-ordering has been removed, since it is no longer maintained and broken"; # added 2023-06-22
+  pytest-openfiles = throw "pytest-openfiles has been removed, since it is unmaintained and archived"; # added 2024-06-19
   pytest-pep8 = pytestpep8; # added 2021-01-04
   pytest-pep257 = throw "pytest-pep257 was removed, as the pep257 package was migrated into pycodestyle"; # added 2022-04-12
   pytest-pythonpath = throw "pytest-pythonpath is obsolete as of pytest 7.0.0 and has been removed"; # added 2022-03-09
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 80b80982805c3..0113f26465f08 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -1393,6 +1393,8 @@ self: super: with self; {
 
   backports-strenum = callPackage ../development/python-modules/backports-strenum { };
 
+  backports-tarfile = callPackage ../development/python-modules/backports-tarfile { };
+
   backports-zoneinfo = callPackage ../development/python-modules/backports-zoneinfo { };
 
   bacpypes = callPackage ../development/python-modules/bacpypes { };
@@ -4147,6 +4149,8 @@ self: super: with self; {
 
   fastapi = callPackage ../development/python-modules/fastapi { };
 
+  fastapi-cli = callPackage ../development/python-modules/fastapi-cli { };
+
   fastapi-mail = callPackage ../development/python-modules/fastapi-mail { };
 
   fastapi-sso = callPackage ../development/python-modules/fastapi-sso { };
@@ -4455,8 +4459,12 @@ self: super: with self; {
 
   flet-runtime = callPackage ../development/python-modules/flet-runtime { };
 
+  flexcache = callPackage ../development/python-modules/flexcache { };
+
   flexmock = callPackage ../development/python-modules/flexmock { };
 
+  flexparser = callPackage ../development/python-modules/flexparser { };
+
   flickrapi = callPackage ../development/python-modules/flickrapi { };
 
   flipr-api = callPackage ../development/python-modules/flipr-api { };
@@ -7621,6 +7629,8 @@ self: super: with self; {
 
   mkdocs-exclude = callPackage ../development/python-modules/mkdocs-exclude { };
 
+  mkdocs-get-deps = callPackage ../development/python-modules/mkdocs-get-deps { };
+
   mkdocs-git-authors-plugin = callPackage ../development/python-modules/mkdocs-git-authors-plugin { };
 
   mkdocs-git-revision-date-localized-plugin = callPackage ../development/python-modules/mkdocs-git-revision-date-localized-plugin { };
@@ -9059,7 +9069,9 @@ self: super: with self; {
 
   numpydoc = callPackage ../development/python-modules/numpydoc { };
 
-  numpy = callPackage ../development/python-modules/numpy { };
+  numpy_1 = callPackage ../development/python-modules/numpy/1.nix { };
+  numpy_2 = callPackage ../development/python-modules/numpy/2.nix { };
+  numpy = if self.pythonOlder "3.13" then numpy_1 else numpy_2;
 
   numpy-stl = callPackage ../development/python-modules/numpy-stl { };
 
@@ -11615,9 +11627,7 @@ self: super: with self; {
 
   phonemizer = callPackage ../development/python-modules/phonemizer { };
 
-  pyopencl = callPackage ../development/python-modules/pyopencl {
-    mesa_drivers = pkgs.mesa.drivers;
-  };
+  pyopencl = callPackage ../development/python-modules/pyopencl { };
 
   pyopengl = callPackage ../development/python-modules/pyopengl { };
 
@@ -12275,6 +12285,8 @@ self: super: with self; {
 
   pytest-lazy-fixture = callPackage ../development/python-modules/pytest-lazy-fixture { };
 
+  pytest-lazy-fixtures = callPackage ../development/python-modules/pytest-lazy-fixtures { };
+
   pytest-localserver = callPackage ../development/python-modules/pytest-localserver { };
 
   pytest-logdog = callPackage ../development/python-modules/pytest-logdog { };
@@ -12297,8 +12309,6 @@ self: super: with self; {
 
   pytest-notebook = callPackage ../development/python-modules/pytest-notebook { };
 
-  pytest-openfiles = callPackage ../development/python-modules/pytest-openfiles { };
-
   pytest-order = callPackage ../development/python-modules/pytest-order { };
 
   pytest-param-files = callPackage ../development/python-modules/pytest-param-files { };
@@ -17337,9 +17347,7 @@ self: super: with self; {
 
   xtensor-python = callPackage ../development/python-modules/xtensor-python { };
 
-  xvfbwrapper = callPackage ../development/python-modules/xvfbwrapper {
-    inherit (pkgs.xorg) xorgserver;
-  };
+  xvfbwrapper = callPackage ../development/python-modules/xvfbwrapper {};
 
   xxhash = callPackage ../development/python-modules/xxhash { };
 
diff --git a/pkgs/top-level/stage.nix b/pkgs/top-level/stage.nix
index 087b43c3cb145..b0c7ec03827b4 100644
--- a/pkgs/top-level/stage.nix
+++ b/pkgs/top-level/stage.nix
@@ -292,7 +292,7 @@ let
           pkgsExtraHardening = super';
           stdenv = super'.withDefaultHardeningFlags (
             super'.stdenv.cc.defaultHardeningFlags ++ [
-              "zerocallusedregs"
+              "stackclashprotection"
               "trivialautovarinit"
             ]
           ) super'.stdenv;