From 9d8e2cb75f69d5185addd49294ff101c2d57d33e Mon Sep 17 00:00:00 2001
From: Emily <vcs@emily.moe>
Date: Fri, 12 Sep 2025 01:20:06 +0100
Subject: [PATCH] python313Packages.pybind11: 2.13.6 -> 3.0.1

Diff: https://github.com/pybind/pybind11/compare/refs/tags/v2.13.6...refs/tags/v3.0.1

Changelog: https://github.com/pybind/pybind11/blob/refs/tags/v3.0.1/docs/changelog.rst

Co-authored-by: Doron Behar <doron.behar@gmail.com>
---
 .../python-modules/pybind11/default.nix       | 106 +++++++++---------
 1 file changed, 53 insertions(+), 53 deletions(-)

diff --git a/pkgs/development/python-modules/pybind11/default.nix b/pkgs/development/python-modules/pybind11/default.nix
index e7f4b9055db4..4ce742c363ff 100644
--- a/pkgs/development/python-modules/pybind11/default.nix
+++ b/pkgs/development/python-modules/pybind11/default.nix
@@ -6,13 +6,14 @@
   fetchFromGitHub,
   cmake,
   ninja,
-  setuptools,
+  scikit-build-core,
+  pybind11,
   boost,
   eigen,
   python,
   catch2,
   numpy,
-  pytestCheckHook,
+  pytest,
   libxcrypt,
   makeSetupHook,
 }:
@@ -29,80 +30,79 @@ let
 in
 buildPythonPackage rec {
   pname = "pybind11";
-  version = "2.13.6";
+  version = "3.0.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "pybind";
     repo = "pybind11";
     tag = "v${version}";
-    hash = "sha256-SNLdtrOjaC3lGHN9MAqTf51U9EzNKQLyTMNPe0GcdrU=";
+    hash = "sha256-ZiwNGsE1FOkhnWv/1ib1akhQ4FZvrXRCDnnBZoPp6r4=";
   };
 
   build-system = [
     cmake
     ninja
-    setuptools
+    pybind11.passthru.scikit-build-core-no-tests
+  ];
+
+  buildInputs = [
+    # Used only for building tests - something we do even when cross
+    # compiling.
+    catch2
+    boost
+    eigen
   ];
 
-  buildInputs = lib.optionals (pythonOlder "3.9") [ libxcrypt ];
   propagatedNativeBuildInputs = [ setupHook ];
 
-  dontUseCmakeBuildDir = true;
+  nativeCheckInputs = [
+    numpy
+    pytest
+  ];
 
-  # Don't build tests if not needed, read the doInstallCheck value at runtime
-  preConfigure = ''
-    if [ -n "$doInstallCheck" ]; then
-      cmakeFlagsArray+=("-DBUILD_TESTING=ON")
-    fi
-  '';
+  pypaBuildFlags = [
+    # Keep the build directory around to run the tests.
+    "-Cbuild-dir=build"
+  ];
 
   cmakeFlags = [
-    "-DBoost_INCLUDE_DIR=${lib.getDev boost}/include"
-    "-DCATCH_INCLUDE_DIR=${lib.getDev catch2}/include/catch2"
-    "-DEIGEN3_INCLUDE_DIR=${lib.getDev eigen}/include/eigen3"
-  ]
-  ++ lib.optionals (python.isPy3k && !stdenv.cc.isClang) [ "-DPYBIND11_CXX_STANDARD=-std=c++17" ];
+    # Always build tests, because even when cross compiling building the tests
+    # is another confirmation that everything is OK.
+    (lib.cmakeBool "BUILD_TESTING" true)
 
-  postBuild = ''
-    # build tests
-    make -j $NIX_BUILD_CORES
-  '';
+    # Override the `PYBIND11_NOPYTHON = true` in `pyproject.toml`. This
+    # is required to build the tests.
+    (lib.cmakeBool "PYBIND11_NOPYTHON" false)
+  ];
 
+  dontUseCmakeConfigure = true;
+
+  ninjaFlags = [
+    "-C"
+    "build"
+  ];
+
+  checkTarget = "check";
+
+  checkPhase = "ninjaCheckPhase";
+
+  # Make the headers and CMake/pkg-config files inside the wheel
+  # discoverable. This simulates the effect of the `pybind11[global]`
+  # installation but works better for our build.
   postInstall = ''
-    make install
-    # Symlink the CMake-installed headers to the location expected by setuptools
-    mkdir -p $out/include/${python.libPrefix}
-    ln -sf $out/include/pybind11 $out/include/${python.libPrefix}/pybind11
+    ln -s $out/${python.sitePackages}/pybind11/{include,share} $out/
   '';
 
-  nativeCheckInputs = [
-    catch2
-    numpy
-    pytestCheckHook
-  ];
-
-  disabledTestPaths = [
-    # require dependencies not available in nixpkgs
-    "tests/test_embed/test_trampoline.py"
-    "tests/test_embed/test_interpreter.py"
-    # numpy changed __repr__ output of numpy dtypes
-    "tests/test_numpy_dtypes.py"
-    # no need to test internal packaging
-    "tests/extra_python_package/test_files.py"
-    # tests that try to parse setuptools stdout
-    "tests/extra_setuptools/test_setuphelper.py"
-  ];
-
-  disabledTests = lib.optionals stdenv.hostPlatform.isDarwin [
-    # expects KeyError, gets RuntimeError
-    # https://github.com/pybind/pybind11/issues/4243
-    "test_cross_module_exception_translator"
-  ];
-
-  postCheck = ''
-    make cpptest
-  '';
+  passthru = {
+    # scikit-build-core's tests depend upon pybind11, and hence introduce
+    # infinite recursion. To avoid this, we define here a scikit-build-core
+    # derivation that doesn't depend on pybind11, and use it for pybind11's
+    # build-system.
+    scikit-build-core-no-tests = scikit-build-core.overridePythonAttrs {
+      doCheck = false;
+    };
+  };
 
   hardeningDisable = lib.optional stdenv.hostPlatform.isMusl "fortify";