Deprecate mixing Python environments using --paths=.../site-packages

And add some XKCD-1987 themed *current python environment* hints into the
logs.

PyInstaller/__main__.py

@@ -191,6 +191,7 @@ def run(pyi_args: list | None = None, pyi_config: dict | None = None):
         logger.info('PyInstaller: %s, contrib hooks: %s', __version__, contrib_hooks_version)
         logger.info('Python: %s%s', platform.python_version(), " (conda)" if compat.is_conda else "")
         logger.info('Platform: %s', platform.platform())
+        logger.info('Python environment: %s', sys.prefix)
 
         # Skip creating .spec when .spec file is supplied.
         if args.filenames[0].endswith('.spec'):

PyInstaller/building/build_main.py

@@ -20,7 +20,7 @@
 import pprint
 import shutil
 import enum
-
+import re
 import sys
 
 from PyInstaller import DEFAULT_DISTPATH, DEFAULT_WORKPATH, HOMEPATH, compat
@@ -455,13 +455,25 @@ def __init__(
         # Django hook requires this variable to find the script manage.py.
         CONF['main_script'] = self.inputs[0]
 
+        for path in (pathex or []):
+            if pathlib.Path(path).name == "site-packages":
+                logger.log(
+                    logging.DEPRECATION,
+                    "Foreign Python environment's site-packages (%s) added to --paths/pathex. This is ALWAYS the wrong "
+                    "thing to do. If your environment's site-packages is not in PyInstaller's module search path then "
+                    "you are running PyInstaller from a different environment to the one your packages are in. Run "
+                    "print(sys.prefix) without PyInstaller to get the environment you should be using then install and "
+                    "run PyInstaller from that environment instead of this one. This warning will become an error in "
+                    "PyInstaller 7.0.", path
+                )
+
         self.pathex = self._extend_pathex(pathex, self.inputs)
         # Set global config variable 'pathex' to make it available for PyInstaller.utils.hooks and import hooks. Path
         # extensions for module search.
         CONF['pathex'] = self.pathex
         # Extend sys.path so PyInstaller could find all necessary modules.
-        logger.info('Extending PYTHONPATH with paths\n' + pprint.pformat(self.pathex))
         sys.path.extend(self.pathex)
+        logger.info('Module search paths (PYTHONPATH):\n' + pprint.pformat(sys.path))
 
         self.hiddenimports = hiddenimports or []
         # Include hidden imports passed via CONF['hiddenimports']; these might be populated if user has a wrapper script

news/0.deprecation.2.rst

@@ -0,0 +1 @@
+Adding a Python environment's ``site-packages`` directory to ``pathex``/``--paths`` will be blocked in v7.0