Remove hardcoded libpython binaries and add debug step

venv/lib/python3.12/site-packages/PyInstaller/hooks/hook-scipy.spatial._ckdtree.py

@@ -0,0 +1,16 @@
+#-----------------------------------------------------------------------------
+# Copyright (c) 2025, PyInstaller Development Team.
+#
+# Distributed under the terms of the GNU General Public License (version 2
+# or later) with exception for distributing the bootloader.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#
+# SPDX-License-Identifier: (GPL-2.0-or-later WITH Bootloader-exception)
+#-----------------------------------------------------------------------------
+
+from PyInstaller.utils.hooks import is_module_satisfies
+
+# As of SciPy 1.16.0, `scipy.spatial._ckdtree` extension started to depend on newly-introduced `scipy._cyutility`.
+if is_module_satisfies('scipy >= 1.16.0'):
+    hiddenimports = ['scipy._cyutility']