diff --git a/pkgs/development/python-modules/hoomd-blue/default.nix b/pkgs/development/python-modules/hoomd-blue/default.nix
index ebadd5552698..28836e4854ce 100644
--- a/pkgs/development/python-modules/hoomd-blue/default.nix
+++ b/pkgs/development/python-modules/hoomd-blue/default.nix
@@ -1,6 +1,6 @@
 {
   lib,
-  stdenv,
+  buildPythonPackage,
   fetchgit,
   cmake,
   pkgconfig,
@@ -19,9 +19,10 @@ let
   onOffBool = b: if b then "ON" else "OFF";
   withMPI = (mpi != null);
 in
-stdenv.mkDerivation rec {
+buildPythonPackage rec {
   version = "2.3.4";
   pname = "hoomd-blue";
+  pyproject = false; # Built with cmake
 
   src = fetchgit {
     url = "https://bitbucket.org/glotzer/hoomd-blue";
diff --git a/pkgs/development/python-modules/py3buddy/default.nix b/pkgs/development/python-modules/py3buddy/default.nix
index 33a5cfc593a3..e076aa3b667e 100644
--- a/pkgs/development/python-modules/py3buddy/default.nix
+++ b/pkgs/development/python-modules/py3buddy/default.nix
@@ -1,23 +1,24 @@
 {
   lib,
-  stdenv,
+  buildPythonPackage,
   fetchFromGitHub,
   python,
   pyusb,
 }:
 
-stdenv.mkDerivation (finalAttrs: {
+buildPythonPackage rec {
   pname = "py3buddy";
   version = "1.0";
+  pyproject = false; # manually installed
 
   src = fetchFromGitHub {
     owner = "armijnhemel";
     repo = "py3buddy";
-    rev = finalAttrs.version;
+    rev = version;
     hash = "sha256-KJ0xGEXHY6o2074WFZ0u7gATS+wrrjyzanYretckWYk=";
   };
 
-  propagatedBuildInputs = [ pyusb ];
+  dependencies = [ pyusb ];
 
   dontConfigure = true;
   dontBuild = true;
@@ -40,4 +41,4 @@ stdenv.mkDerivation (finalAttrs: {
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ prusnak ];
   };
-})
+}
diff --git a/pkgs/tools/networking/unbound/python.nix b/pkgs/development/python-modules/pyunbound/default.nix
similarity index 92%
rename from pkgs/tools/networking/unbound/python.nix
rename to pkgs/development/python-modules/pyunbound/default.nix
index 94f2374d904d..a5d33cbfa440 100644
--- a/pkgs/tools/networking/unbound/python.nix
+++ b/pkgs/development/python-modules/pyunbound/default.nix
@@ -1,11 +1,10 @@
-{ lib, stdenv, unbound, openssl, expat, libevent, swig, pythonPackages }:
+{ lib, buildPythonPackage, unbound, openssl, expat, libevent, swig, python, stdenv }:
 
-let
-  inherit (pythonPackages) python;
-in
-stdenv.mkDerivation rec {
+buildPythonPackage rec {
   pname = "pyunbound";
   inherit (unbound) version src;
+  pyproject = false; # Built with configure script
+
   patches = unbound.patches or null;
 
   nativeBuildInputs = [ swig ];
diff --git a/pkgs/development/python-modules/segyio/add_missing_cstdint.patch b/pkgs/development/python-modules/segyio/add_missing_cstdint.patch
new file mode 100644
index 000000000000..2c26d6e454b1
--- /dev/null
+++ b/pkgs/development/python-modules/segyio/add_missing_cstdint.patch
@@ -0,0 +1,47 @@
+From 64f06c0643f1f8691a8f2757496b60f1ab98c866 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Sa=C3=AFd=20Benaissa?= <sbenaissa@shearwatergeo.com>
+Date: Fri, 8 Dec 2023 21:51:32 +0100
+Subject: [PATCH] Add include for cstdint, fix segyio build on fedora
+
+---
+ lib/experimental/segyio/segyio.hpp | 1 +
+ python/segyio/segyio.cpp           | 1 +
+ python/setup.py                    | 2 +-
+ 3 files changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/lib/experimental/segyio/segyio.hpp b/lib/experimental/segyio/segyio.hpp
+index 706f07ff5..7ba3ffb99 100644
+--- a/lib/experimental/segyio/segyio.hpp
++++ b/lib/experimental/segyio/segyio.hpp
+@@ -13,6 +13,7 @@
+ #include <vector>
+ 
+ #include <segyio/segy.h>
++#include <cstdint>
+ 
+ /*
+  * KNOWN ISSUES AND TODOs:
+diff --git a/python/segyio/segyio.cpp b/python/segyio/segyio.cpp
+index 76da965c3..bd8a8622e 100644
+--- a/python/segyio/segyio.cpp
++++ b/python/segyio/segyio.cpp
+@@ -16,6 +16,7 @@
+ #include <cstring>
+ #include <sstream>
+ #include <stdexcept>
++#include <cstdint>
+ 
+ #if PY_MAJOR_VERSION >= 3
+ #define IS_PY3K
+diff --git a/python/setup.py b/python/setup.py
+index 6c6553bc7..654075be9 100644
+--- a/python/setup.py
++++ b/python/setup.py
+@@ -1,6 +1,6 @@
+ import os
+ import sys
+-import skbuild
++import skbuild  # pip install scikit-build
+ import setuptools
+ 
+ long_description = """
diff --git a/pkgs/development/python-modules/segyio/default.nix b/pkgs/development/python-modules/segyio/default.nix
index aba2d06a5e2a..9e221db8cfe7 100644
--- a/pkgs/development/python-modules/segyio/default.nix
+++ b/pkgs/development/python-modules/segyio/default.nix
@@ -1,18 +1,23 @@
 {
   lib,
-  stdenv,
+  buildPythonPackage,
   fetchFromGitHub,
   cmake,
   ninja,
-  python,
   scikit-build,
   pytest,
   numpy,
 }:
 
-stdenv.mkDerivation rec {
+buildPythonPackage rec {
   pname = "segyio";
   version = "1.9.12";
+  pyproject = false; # Built with cmake
+
+  patches = [
+    # https://github.com/equinor/segyio/pull/570
+    ./add_missing_cstdint.patch
+  ];
 
   postPatch = ''
     # Removing unecessary build dependency
@@ -34,7 +39,6 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [
     cmake
     ninja
-    python
     scikit-build
   ];
 
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 16ffb80ef7e9..4837be366cb2 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -2587,7 +2587,7 @@ self: super: with self; {
 
   criticality-score = callPackage ../development/python-modules/criticality-score { };
 
-  crocoddyl = toPythonModule (callPackage ../development/libraries/crocoddyl {
+  crocoddyl = toPythonModule (pkgs.crocoddyl.override {
     pythonSupport = true;
     python3Packages = self;
   });
@@ -4932,7 +4932,8 @@ self: super: with self; {
 
   gmpy = callPackage ../development/python-modules/gmpy { };
 
-  gmsh = toPythonModule (callPackage ../applications/science/math/gmsh {
+  gmsh = toPythonModule (pkgs.gmsh.override {
+    inherit (self) python;
     enablePython = true;
   });
 
@@ -5522,9 +5523,7 @@ self: super: with self; {
 
   homepluscontrol = callPackage ../development/python-modules/homepluscontrol { };
 
-  hoomd-blue = toPythonModule (callPackage ../development/python-modules/hoomd-blue {
-    inherit python;
-  });
+  hoomd-blue = callPackage ../development/python-modules/hoomd-blue { };
 
   hopcroftkarp = callPackage ../development/python-modules/hopcroftkarp { };
 
@@ -6513,6 +6512,7 @@ self: super: with self; {
 
   kmsxx = toPythonModule (pkgs.kmsxx.override {
     withPython = true;
+    python3Packages = self;
   });
 
   knack = callPackage ../development/python-modules/knack { };
@@ -8867,7 +8867,7 @@ self: super: with self; {
 
   neuron-full = pkgs.neuron-full.override { python3 = python; };
 
-  neuronpy = python.pkgs.toPythonModule neuron-full;
+  neuronpy = toPythonModule neuron-full;
 
   nevow = callPackage ../development/python-modules/nevow { };
 
@@ -9681,7 +9681,7 @@ self: super: with self; {
 
   pbs-installer = callPackage ../development/python-modules/pbs-installer { };
 
-  pc-ble-driver-py = toPythonModule (callPackage ../development/python-modules/pc-ble-driver-py { });
+  pc-ble-driver-py = callPackage ../development/python-modules/pc-ble-driver-py { };
 
   pcapy-ng = callPackage ../development/python-modules/pcapy-ng {
     inherit (pkgs) libpcap; # Avoid confusion with python package of the same name
@@ -10713,7 +10713,7 @@ self: super: with self; {
 
   py2bit = callPackage ../development/python-modules/py2bit { };
 
-  py3buddy = toPythonModule (callPackage ../development/python-modules/py3buddy { });
+  py3buddy = callPackage ../development/python-modules/py3buddy { };
 
   py3exiv2 = callPackage ../development/python-modules/py3exiv2 {
     inherit (pkgs) exiv2;
@@ -12831,7 +12831,7 @@ self: super: with self; {
     inherit (pkgs) udev;
   };
 
-  pyunbound = toPythonModule (callPackage ../tools/networking/unbound/python.nix { });
+  pyunbound = callPackage ../development/python-modules/pyunbound { };
 
   pyunifi = callPackage ../development/python-modules/pyunifi { };
 
@@ -13875,9 +13875,9 @@ self: super: with self; {
 
   segno = callPackage ../development/python-modules/segno { };
 
-  segyio = toPythonModule (callPackage ../development/python-modules/segyio {
+  segyio = callPackage ../development/python-modules/segyio {
     inherit (pkgs) cmake ninja;
-  });
+  };
 
   selectors2 = callPackage ../development/python-modules/selectors2 { };
 
@@ -15389,7 +15389,7 @@ self: super: with self; {
     inherit (pkgs.darwin.apple_sdk.frameworks) Security;
   };
 
-  tokenize-rt = toPythonModule (callPackage ../development/python-modules/tokenize-rt { });
+  tokenize-rt = callPackage ../development/python-modules/tokenize-rt { };
 
   tokenlib = callPackage ../development/python-modules/tokenlib { };
 
@@ -16854,7 +16854,9 @@ self: super: with self; {
 
   vidstab = callPackage ../development/python-modules/vidstab { };
 
-  viennarna = toPythonModule pkgs.viennarna;
+  viennarna = toPythonModule (pkgs.viennarna.override {
+    python3 = self.python;
+  });
 
   viewstate = callPackage ../development/python-modules/viewstate { };