diff --git a/pkgs/development/python-modules/pybind11/default.nix b/pkgs/development/python-modules/pybind11/default.nix
index cfb7d42a6f46..1a06de633b68 100644
--- a/pkgs/development/python-modules/pybind11/default.nix
+++ b/pkgs/development/python-modules/pybind11/default.nix
@@ -4,6 +4,8 @@
 , pythonOlder
 , fetchFromGitHub
 , cmake
+, ninja
+, setuptools
 , boost
 , eigen
 , python
@@ -37,23 +39,29 @@
     else python.stdenv;
 in buildPythonPackage rec {
   pname = "pybind11";
-  version = "2.11.1";
-  format = "setuptools";
+  version = "2.12.0";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "pybind";
-    repo = pname;
+    repo = "pybind11";
     rev = "v${version}";
-    hash = "sha256-sO/Fa+QrAKyq2EYyYMcjPrYI+bdJIrDoj6L3JHoDo3E=";
+    hash = "sha256-DVkI5NxM5uME9m3PFYVpJOOa2j+yjL6AJn76fCTv2nE=";
   };
 
   postPatch = ''
-    sed -i "/^timeout/d" pyproject.toml
+    substituteInPlace pyproject.toml \
+      --replace-fail "timeout=300" ""
   '';
 
-  nativeBuildInputs = [ cmake ];
+  build-system = [
+    cmake
+    ninja
+    setuptools
+  ];
+
   buildInputs = lib.optionals (pythonOlder "3.9") [ libxcrypt ];
-  propagatedBuildInputs = [ setupHook ];
+  propagatedNativeBuildInputs = [ setupHook ];
 
   stdenv = stdenv';
 
diff --git a/pkgs/development/python-modules/scipy/default.nix b/pkgs/development/python-modules/scipy/default.nix
index 2587ada7e570..b4be27dcd531 100644
--- a/pkgs/development/python-modules/scipy/default.nix
+++ b/pkgs/development/python-modules/scipy/default.nix
@@ -34,8 +34,8 @@ let
   #     nix-shell maintainers/scripts/update.nix --argstr package python3.pkgs.scipy
   #
   # The update script uses sed regexes to replace them with the updated hashes.
-  version = "1.12.0";
-  srcHash = "sha256-PuiyYTgSegDTV9Kae5N68FOXT1jyJrNv9p2aFP70Z20=";
+  version = "1.13.0";
+  srcHash = "sha256-HaYk92hOREHMOXppK+Bs9DrBu9KUVUsZ0KV+isTofUo=";
   datasetsHashes = {
     ascent = "1qjp35ncrniq9rhzb14icwwykqg2208hcssznn3hz27w39615kh3";
     ecg = "1bwbjp43b7znnwha5hv6wiz3g0bhwrpqpi75s12zidxrbwvd62pj";
@@ -76,18 +76,15 @@ in buildPythonPackage {
         "doc/source/dev/contributor/meson_advanced.rst"
       ];
     })
-    (fetchpatch {
-      name = "openblas-0.3.26-compat.patch";
-      url = "https://github.com/scipy/scipy/commit/8c96a1f742335bca283aae418763aaba62c03378.patch";
-      hash = "sha256-SGoYDxwSAkr6D5/XEqHLerF4e4nmmI+PX+z+3taWAps=";
-    })
   ];
 
-  # Upstream complicated numpy version pinning is causing issues in the
-  # configurePhase, so we pass on it.
+  # Upstream says in a comment in their pyproject.toml that building against
+  # both numpy 2 and numpy 1 should work, but they seem to worry about numpy
+  # incompatibilities that we here with Nixpkgs' Python ecosystem, shouldn't
+  # experience.
   postPatch = ''
     substituteInPlace pyproject.toml \
-      --replace-fail 'numpy==' 'numpy>=' \
+      --replace-fail 'numpy>=2.0.0rc1,' 'numpy' \
   '';
 
   nativeBuildInputs = [