GH-126985: move pyvenv.cfg detection from site to getpath (#126987)

Doc/c-api/init_config.rst

@@ -1590,9 +1590,22 @@ If a ``._pth`` file is present:
 * Set :c:member:`~PyConfig.site_import` to ``0``.
 * Set :c:member:`~PyConfig.safe_path` to ``1``.
 
+If :c:member:`~PyConfig.home` is not set and a ``pyvenv.cfg`` file is present in
+the same directory as :c:member:`~PyConfig.executable`, or its parent,
+:c:member:`~PyConfig.prefix` and :c:member:`~PyConfig.exec_prefix` are set that
+location. When this happens, :c:member:`~PyConfig.base_prefix` and
+:c:member:`~PyConfig.base_exec_prefix` still keep their value, pointing to the
+base installation. See :ref:`sys-path-init-virtual-environments` for more
+information.
+
 The ``__PYVENV_LAUNCHER__`` environment variable is used to set
 :c:member:`PyConfig.base_executable`.
 
+.. versionchanged:: 3.14
+
+   :c:member:`~PyConfig.prefix`, and :c:member:`~PyConfig.exec_prefix`, are now
+   set to the ``pyvenv.cfg`` directory. This was previously done by :mod:`site`,
+   therefore affected by :option:`-S`.
 
 .. _pyinitconfig_api:
 

Doc/library/site.rst

@@ -49,14 +49,22 @@ added path for configuration files.
    identified by the "t" suffix in the version-specific directory name, such as
    :file:`lib/python3.13t/`.
 
-If a file named "pyvenv.cfg" exists one directory above sys.executable,
+.. versionchanged:: 3.14
-sys.prefix and sys.exec_prefix are set to that directory and
+
-it is also checked for site-packages (sys.base_prefix and
+   :mod:`site` is no longer responsible for updating :data:`sys.prefix` and
-sys.base_exec_prefix will always be the "real" prefixes of the Python
+   :data:`sys.exec_prefix` on :ref:`sys-path-init-virtual-environments`. This is
-installation). If "pyvenv.cfg" (a bootstrap configuration file) contains
+   now done during the :ref:`path initialization <sys-path-init>`. As a result,
-the key "include-system-site-packages" set to anything other than "true"
+   under :ref:`sys-path-init-virtual-environments`, :data:`sys.prefix` and
-(case-insensitive), the system-level prefixes will not be
+   :data:`sys.exec_prefix` no longer depend on the :mod:`site` initialization,
-searched for site-packages; otherwise they will.
+   and are therefore unaffected by :option:`-S`.
+
+.. _site-virtual-environments-configuration:
+
+When running under a :ref:`virtual environment <sys-path-init-virtual-environments>`,
+the ``pyvenv.cfg`` file in :data:`sys.prefix` is checked for site-specific
+configurations. If the ``include-system-site-packages`` key exists and is set to
+``true`` (case-insensitive), the system-level prefixes will be searched for
+site-packages, otherwise they won't.
 
 .. index::
    single: # (hash); comment

Doc/library/sys.rst

@@ -130,27 +130,26 @@ always available.
 
 .. data:: base_exec_prefix
 
-   Set during Python startup, before ``site.py`` is run, to the same value as
+   Equivalent to :data:`exec_prefix`, but refering to the base Python installation.
-   :data:`exec_prefix`. If not running in a
+
-   :ref:`virtual environment <venv-def>`, the values will stay the same; if
+   When running under :ref:`sys-path-init-virtual-environments`,
-   ``site.py`` finds that a virtual environment is in use, the values of
+   :data:`exec_prefix` gets overwritten to the virtual environment prefix.
-   :data:`prefix` and :data:`exec_prefix` will be changed to point to the
+   :data:`base_exec_prefix`, conversely, does not change, and always points to
-   virtual environment, whereas :data:`base_prefix` and
+   the base Python installation.
-   :data:`base_exec_prefix` will remain pointing to the base Python
+   Refer to :ref:`sys-path-init-virtual-environments` for more information.
-   installation (the one which the virtual environment was created from).
 
    .. versionadded:: 3.3
 
 
 .. data:: base_prefix
 
-   Set during Python startup, before ``site.py`` is run, to the same value as
+   Equivalent to :data:`prefix`, but refering to the base Python installation.
-   :data:`prefix`. If not running in a :ref:`virtual environment <venv-def>`, the values
+
-   will stay the same; if ``site.py`` finds that a virtual environment is in
+   When running under :ref:`virtual environment <venv-def>`,
-   use, the values of :data:`prefix` and :data:`exec_prefix` will be changed to
+   :data:`prefix` gets overwritten to the virtual environment prefix.
-   point to the virtual environment, whereas :data:`base_prefix` and
+   :data:`base_prefix`, conversely, does not change, and always points to
-   :data:`base_exec_prefix` will remain pointing to the base Python
+   the base Python installation.
-   installation (the one which the virtual environment was created from).
+   Refer to :ref:`sys-path-init-virtual-environments` for more information.
 
    .. versionadded:: 3.3
 
@@ -483,11 +482,19 @@ always available.
 
    .. note::
 
-      If a :ref:`virtual environment <venv-def>` is in effect, this
+      If a :ref:`virtual environment <venv-def>` is in effect, this :data:`exec_prefix`
-      value will be changed in ``site.py`` to point to the virtual environment.
+      will point to the virtual environment. The value for the Python installation
-      The value for the Python installation will still be available, via
+      will still be available, via :data:`base_exec_prefix`.
-      :data:`base_exec_prefix`.
+      Refer to :ref:`sys-path-init-virtual-environments` for more information.
 
+   .. versionchanged:: 3.14
+
+      When running under a :ref:`virtual environment <venv-def>`,
+      :data:`prefix` and :data:`exec_prefix` are now set to the virtual
+      environment prefix by the :ref:`path initialization <sys-path-init>`,
+      instead of :mod:`site`. This means that :data:`prefix` and
+      :data:`exec_prefix` always point to the virtual environment, even when
+      :mod:`site` is disabled (:option:`-S`).
 
 .. data:: executable
 
@@ -1483,10 +1490,21 @@ always available.
    argument to the :program:`configure` script.  See
    :ref:`installation_paths` for derived paths.
 
-   .. note:: If a :ref:`virtual environment <venv-def>` is in effect, this
+   .. note::
-      value will be changed in ``site.py`` to point to the virtual
+
-      environment. The value for the Python installation will still be
+      If a :ref:`virtual environment <venv-def>` is in effect, this :data:`prefix`
-      available, via :data:`base_prefix`.
+      will point to the virtual environment. The value for the Python installation
+      will still be available, via :data:`base_prefix`.
+      Refer to :ref:`sys-path-init-virtual-environments` for more information.
+
+   .. versionchanged:: 3.14
+
+      When running under a :ref:`virtual environment <venv-def>`,
+      :data:`prefix` and :data:`exec_prefix` are now set to the virtual
+      environment prefix by the :ref:`path initialization <sys-path-init>`,
+      instead of :mod:`site`. This means that :data:`prefix` and
+      :data:`exec_prefix` always point to the virtual environment, even when
+      :mod:`site` is disabled (:option:`-S`).
 
 
 .. data:: ps1

Doc/library/sys_path_init.rst

@@ -47,8 +47,15 @@ however on other platforms :file:`lib/python{majorversion}.{minorversion}/lib-dy
 ``exec_prefix``. On some platforms :file:`lib` may be :file:`lib64` or another value,
 see :data:`sys.platlibdir` and :envvar:`PYTHONPLATLIBDIR`.
 
-Once found, ``prefix`` and ``exec_prefix`` are available at :data:`sys.prefix` and
+Once found, ``prefix`` and ``exec_prefix`` are available at
-:data:`sys.exec_prefix` respectively.
+:data:`sys.base_prefix` and :data:`sys.base_exec_prefix` respectively.
+
+If :envvar:`PYTHONHOME` is not set, and a ``pyvenv.cfg`` file is found alongside
+the main executable, or in its parent directory, :data:`sys.prefix` and
+:data:`sys.exec_prefix` get set to the directory containing ``pyvenv.cfg``,
+otherwise they are set to the same value as :data:`sys.base_prefix` and
+:data:`sys.base_exec_prefix`, respectively.
+This is used by :ref:`sys-path-init-virtual-environments`.
 
 Finally, the :mod:`site` module is processed and :file:`site-packages` directories
 are added to the module search path. A common way to customize the search path is
@@ -60,18 +67,40 @@ the :mod:`site` module documentation.
    Certain command line options may further affect path calculations.
    See :option:`-E`, :option:`-I`, :option:`-s` and :option:`-S` for further details.
 
-Virtual environments
+.. versionchanged:: 3.14
+
+   :data:`sys.prefix` and :data:`sys.exec_prefix` are now set to the
+   ``pyvenv.cfg`` directory during the path initialization. This was previously
+   done by :mod:`site`, therefore affected by :option:`-S`.
+
+.. _sys-path-init-virtual-environments:
+
+Virtual Environments
 --------------------
 
-If Python is run in a virtual environment (as described at :ref:`tut-venv`)
+Virtual environments place a ``pyvenv.cfg`` file in their prefix, which causes
-then ``prefix`` and ``exec_prefix`` are specific to the virtual environment.
+:data:`sys.prefix` and :data:`sys.exec_prefix` to point to them, instead of the
+base installation.
 
-If a ``pyvenv.cfg`` file is found alongside the main executable, or in the
+The ``prefix`` and ``exec_prefix`` values of the base installation are available
-directory one level above the executable, the following variations apply:
+at :data:`sys.base_prefix` and :data:`sys.base_exec_prefix`.
 
-* If ``home`` is an absolute path and :envvar:`PYTHONHOME` is not set, this
+As well as being used as a marker to identify virtual environments,
-  path is used instead of the path to the main executable when deducing ``prefix``
+``pyvenv.cfg`` may also be used to configure the :mod:`site` initialization.
-  and ``exec_prefix``.
+Please refer to :mod:`site`'s
+:ref:`virtual environments documentation <site-virtual-environments-configuration>`.
+
+.. note::
+
+   :envvar:`PYTHONHOME` overrides the ``pyvenv.cfg`` detection.
+
+.. note::
+
+   There are other ways how "virtual environments" could be implemented, this
+   documentation referes implementations based on the ``pyvenv.cfg`` mechanism,
+   such as :mod:`venv`. Most virtual environment implementations follow the
+   model set by :mod:`venv`, but there may be exotic implementations that
+   diverge from it.
 
 _pth files
 ----------

Doc/library/venv.rst

@@ -25,6 +25,9 @@ A virtual environment is created on top of an existing
 Python installation, known as the virtual environment's "base" Python, and may
 optionally be isolated from the packages in the base environment,
 so only those explicitly installed in the virtual environment are available.
+See :ref:`sys-path-init-virtual-environments` and :mod:`site`'s
+:ref:`virtual environments documentation <site-virtual-environments-configuration>`
+for more information.
 
 When used from within a virtual environment, common installation tools such as
 :pypi:`pip` will install Python packages into a virtual environment

Lib/site.py

@@ -94,6 +94,12 @@ def _trace(message):
         print(message, file=sys.stderr)
 
 
+def _warn(*args, **kwargs):
+    import warnings
+
+    warnings.warn(*args, **kwargs)
+
+
 def makepath(*paths):
     dir = os.path.join(*paths)
     try:
@@ -619,7 +625,10 @@ def venv(known_paths):
                     elif key == 'home':
                         sys._home = value
 
-        sys.prefix = sys.exec_prefix = site_prefix
+        if sys.prefix != site_prefix:
+            _warn(f'Unexpected value in sys.prefix, expected {site_prefix}, got {sys.prefix}', RuntimeWarning)
+        if sys.exec_prefix != site_prefix:
+            _warn(f'Unexpected value in sys.exec_prefix, expected {site_prefix}, got {sys.exec_prefix}', RuntimeWarning)
 
         # Doing this here ensures venv takes precedence over user-site
         addsitepackages(known_paths, [sys.prefix])

Lib/sysconfig/__init__.py

@@ -173,7 +173,9 @@ _SCHEME_KEYS = ('stdlib', 'platstdlib', 'purelib', 'platlib', 'include',
 _PY_VERSION = sys.version.split()[0]
 _PY_VERSION_SHORT = f'{sys.version_info[0]}.{sys.version_info[1]}'
 _PY_VERSION_SHORT_NO_DOT = f'{sys.version_info[0]}{sys.version_info[1]}'
+_PREFIX = os.path.normpath(sys.prefix)
 _BASE_PREFIX = os.path.normpath(sys.base_prefix)
+_EXEC_PREFIX = os.path.normpath(sys.exec_prefix)
 _BASE_EXEC_PREFIX = os.path.normpath(sys.base_exec_prefix)
 # Mutex guarding initialization of _CONFIG_VARS.
 _CONFIG_VARS_LOCK = threading.RLock()
@@ -465,10 +467,8 @@ def _init_config_vars():
     # Normalized versions of prefix and exec_prefix are handy to have;
     # in fact, these are the standard versions used most places in the
     # Distutils.
-    _PREFIX = os.path.normpath(sys.prefix)
+    _CONFIG_VARS['prefix'] = _PREFIX
-    _EXEC_PREFIX = os.path.normpath(sys.exec_prefix)
+    _CONFIG_VARS['exec_prefix'] = _EXEC_PREFIX
-    _CONFIG_VARS['prefix'] = _PREFIX  # FIXME: This gets overwriten by _init_posix.
-    _CONFIG_VARS['exec_prefix'] = _EXEC_PREFIX  # FIXME: This gets overwriten by _init_posix.
     _CONFIG_VARS['py_version'] = _PY_VERSION
     _CONFIG_VARS['py_version_short'] = _PY_VERSION_SHORT
     _CONFIG_VARS['py_version_nodot'] = _PY_VERSION_SHORT_NO_DOT
@@ -541,7 +541,6 @@ def get_config_vars(*args):
     With arguments, return a list of values that result from looking up
     each argument in the configuration variable dictionary.
     """
-    global _CONFIG_VARS_INITIALIZED
 
     # Avoid claiming the lock once initialization is complete.
     if not _CONFIG_VARS_INITIALIZED:
@@ -552,15 +551,6 @@ def get_config_vars(*args):
             # don't re-enter init_config_vars().
             if _CONFIG_VARS is None:
                 _init_config_vars()
-    else:
-        # If the site module initialization happened after _CONFIG_VARS was
-        # initialized, a virtual environment might have been activated, resulting in
-        # variables like sys.prefix changing their value, so we need to re-init the
-        # config vars (see GH-126789).
-        if _CONFIG_VARS['base'] != os.path.normpath(sys.prefix):
-            with _CONFIG_VARS_LOCK:
-                _CONFIG_VARS_INITIALIZED = False
-                _init_config_vars()
 
     if args:
         vals = []

Lib/test/test_embed.py

@@ -1649,14 +1649,14 @@ class InitConfigTests(EmbeddingTestsMixin, unittest.TestCase):
             config = {
                 'base_prefix': sysconfig.get_config_var("prefix"),
                 'base_exec_prefix': exec_prefix,
-                'exec_prefix': exec_prefix,
+                'exec_prefix': tmpdir,
+                'prefix': tmpdir,
                 'base_executable': base_executable,
                 'executable': executable,
                 'module_search_paths': paths,
             }
             if MS_WINDOWS:
                 config['base_prefix'] = pyvenv_home
-                config['prefix'] = pyvenv_home
                 config['stdlib_dir'] = os.path.join(pyvenv_home, 'Lib')
                 config['use_frozen_modules'] = bool(not support.Py_DEBUG)
             else:

Lib/test/test_getpath.py

@@ -92,8 +92,8 @@ class MockGetPathTests(unittest.TestCase):
         ])
         expected = dict(
             executable=r"C:\venv\Scripts\python.exe",
-            prefix=r"C:\Python",
+            prefix=r"C:\venv",
-            exec_prefix=r"C:\Python",
+            exec_prefix=r"C:\venv",
             base_executable=r"C:\Python\python.exe",
             base_prefix=r"C:\Python",
             base_exec_prefix=r"C:\Python",
@@ -339,8 +339,8 @@ class MockGetPathTests(unittest.TestCase):
         ])
         expected = dict(
             executable="/venv/bin/python",
-            prefix="/usr",
+            prefix="/venv",
-            exec_prefix="/usr",
+            exec_prefix="/venv",
             base_executable="/usr/bin/python",
             base_prefix="/usr",
             base_exec_prefix="/usr",
@@ -371,8 +371,8 @@ class MockGetPathTests(unittest.TestCase):
         ])
         expected = dict(
             executable="/venv/bin/python",
-            prefix="/usr",
+            prefix="/venv",
-            exec_prefix="/usr",
+            exec_prefix="/venv",
             base_executable="/usr/bin/python3",
             base_prefix="/usr",
             base_exec_prefix="/usr",
@@ -404,8 +404,8 @@ class MockGetPathTests(unittest.TestCase):
         ])
         expected = dict(
             executable="/venv/bin/python",
-            prefix="/path/to/non-installed",
+            prefix="/venv",
-            exec_prefix="/path/to/non-installed",
+            exec_prefix="/venv",
             base_executable="/path/to/non-installed/bin/python",
             base_prefix="/path/to/non-installed",
             base_exec_prefix="/path/to/non-installed",
@@ -435,8 +435,8 @@ class MockGetPathTests(unittest.TestCase):
         ])
         expected = dict(
             executable="/venv/bin/python",
-            prefix="/usr",
+            prefix="/venv",
-            exec_prefix="/usr",
+            exec_prefix="/venv",
             base_executable="/usr/bin/python9",
             base_prefix="/usr",
             base_exec_prefix="/usr",
@@ -652,8 +652,8 @@ class MockGetPathTests(unittest.TestCase):
         ])
         expected = dict(
             executable=f"{venv_path}/bin/python",
-            prefix="/Library/Frameworks/Python.framework/Versions/9.8",
+            prefix=venv_path,
-            exec_prefix="/Library/Frameworks/Python.framework/Versions/9.8",
+            exec_prefix=venv_path,
             base_executable="/Library/Frameworks/Python.framework/Versions/9.8/bin/python9.8",
             base_prefix="/Library/Frameworks/Python.framework/Versions/9.8",
             base_exec_prefix="/Library/Frameworks/Python.framework/Versions/9.8",
@@ -697,8 +697,8 @@ class MockGetPathTests(unittest.TestCase):
         ])
         expected = dict(
             executable=f"{venv_path}/bin/python",
-            prefix="/Library/Frameworks/DebugPython.framework/Versions/9.8",
+            prefix=venv_path,
-            exec_prefix="/Library/Frameworks/DebugPython.framework/Versions/9.8",
+            exec_prefix=venv_path,
             base_executable="/Library/Frameworks/DebugPython.framework/Versions/9.8/bin/python9.8",
             base_prefix="/Library/Frameworks/DebugPython.framework/Versions/9.8",
             base_exec_prefix="/Library/Frameworks/DebugPython.framework/Versions/9.8",
@@ -734,8 +734,8 @@ class MockGetPathTests(unittest.TestCase):
         ])
         expected = dict(
             executable="/framework/Python9.8/python",
-            prefix="/usr",
+            prefix="/framework/Python9.8",
-            exec_prefix="/usr",
+            exec_prefix="/framework/Python9.8",
             base_executable="/usr/bin/python",
             base_prefix="/usr",
             base_exec_prefix="/usr",

Lib/test/test_sysconfig.py

@@ -110,6 +110,7 @@ class TestSysConfig(unittest.TestCase):
             **venv_create_args,
         )
 
+
     def test_get_path_names(self):
         self.assertEqual(get_path_names(), sysconfig._SCHEME_KEYS)
 
@@ -591,71 +592,6 @@ class TestSysConfig(unittest.TestCase):
         suffix = sysconfig.get_config_var('EXT_SUFFIX')
         self.assertTrue(suffix.endswith('-darwin.so'), suffix)
 
-    @requires_subprocess()
-    def test_config_vars_depend_on_site_initialization(self):
-        script = textwrap.dedent("""
-            import sysconfig
-
-            config_vars = sysconfig.get_config_vars()
-
-            import json
-            print(json.dumps(config_vars, indent=2))
-        """)
-
-        with self.venv() as venv:
-            site_config_vars = json.loads(venv.run('-c', script).stdout)
-            no_site_config_vars = json.loads(venv.run('-S', '-c', script).stdout)
-
-        self.assertNotEqual(site_config_vars, no_site_config_vars)
-        # With the site initialization, the virtual environment should be enabled.
-        self.assertEqual(site_config_vars['base'], venv.prefix)
-        self.assertEqual(site_config_vars['platbase'], venv.prefix)
-        #self.assertEqual(site_config_vars['prefix'], venv.prefix)  # # FIXME: prefix gets overwriten by _init_posix
-        # Without the site initialization, the virtual environment should be disabled.
-        self.assertEqual(no_site_config_vars['base'], site_config_vars['installed_base'])
-        self.assertEqual(no_site_config_vars['platbase'], site_config_vars['installed_platbase'])
-
-    @requires_subprocess()
-    def test_config_vars_recalculation_after_site_initialization(self):
-        script = textwrap.dedent("""
-            import sysconfig
-
-            before = sysconfig.get_config_vars()
-
-            import site
-            site.main()
-
-            after = sysconfig.get_config_vars()
-
-            import json
-            print(json.dumps({'before': before, 'after': after}, indent=2))
-        """)
-
-        with self.venv() as venv:
-            config_vars = json.loads(venv.run('-S', '-c', script).stdout)
-
-        self.assertNotEqual(config_vars['before'], config_vars['after'])
-        self.assertEqual(config_vars['after']['base'], venv.prefix)
-        #self.assertEqual(config_vars['after']['prefix'], venv.prefix)  # FIXME: prefix gets overwriten by _init_posix
-        #self.assertEqual(config_vars['after']['exec_prefix'], venv.prefix)  # FIXME: exec_prefix gets overwriten by _init_posix
-
-    @requires_subprocess()
-    def test_paths_depend_on_site_initialization(self):
-        script = textwrap.dedent("""
-            import sysconfig
-
-            paths = sysconfig.get_paths()
-
-            import json
-            print(json.dumps(paths, indent=2))
-        """)
-
-        with self.venv() as venv:
-            site_paths = json.loads(venv.run('-c', script).stdout)
-            no_site_paths = json.loads(venv.run('-S', '-c', script).stdout)
-
-        self.assertNotEqual(site_paths, no_site_paths)
-
     @requires_subprocess()
     def test_makefile_overwrites_config_vars(self):
         script = textwrap.dedent("""
@@ -689,7 +625,6 @@ class TestSysConfig(unittest.TestCase):
         self.assertNotEqual(data['prefix'], data['base_prefix'])
         self.assertNotEqual(data['exec_prefix'], data['base_exec_prefix'])
 
-
 class MakefileTests(unittest.TestCase):
 
     @unittest.skipIf(sys.platform.startswith('win'),

Misc/NEWS.d/next/Library/2024-11-18-23-42-06.gh-issue-126985.7XplY9.rst

@@ -0,0 +1,3 @@
+When running under a virtual environment with the :mod:`site` disabled (see
+:option:`-S`), :data:`sys.prefix` and :data:`sys.base_prefix` will now point
+to the virtual environment, instead of the base installation.

Modules/getpath.py

@@ -640,11 +640,20 @@ else:
 
 
 # For a venv, update the main prefix/exec_prefix but leave the base ones unchanged
-# XXX: We currently do not update prefix here, but it happens in site.py
+if venv_prefix:
-#if venv_prefix:
+    if not base_prefix:
-#    base_prefix = prefix
+        base_prefix = prefix
-#    base_exec_prefix = exec_prefix
+    if not base_exec_prefix:
-#    prefix = exec_prefix = venv_prefix
+        base_exec_prefix = exec_prefix
+    prefix = exec_prefix = venv_prefix
+
+
+# After calculating prefix and exec_prefix, use their values for base_prefix and
+# base_exec_prefix if they haven't been set.
+if not base_prefix:
+    base_prefix = prefix
+if not base_exec_prefix:
+    base_exec_prefix = exec_prefix
 
 
 # ******************************************************************************
@@ -679,7 +688,7 @@ elif not pythonpath_was_set:
         # QUIRK: POSIX uses the default prefix when in the build directory
         pythonpath.append(joinpath(PREFIX, ZIP_LANDMARK))
     else:
-        pythonpath.append(joinpath(prefix, ZIP_LANDMARK))
+        pythonpath.append(joinpath(base_prefix, ZIP_LANDMARK))
 
     if os_name == 'nt' and use_environment and winreg:
         # QUIRK: Windows also lists paths in the registry. Paths are stored
@@ -714,13 +723,13 @@ elif not pythonpath_was_set:
     # Then add any entries compiled into the PYTHONPATH macro.
     if PYTHONPATH:
         for p in PYTHONPATH.split(DELIM):
-            pythonpath.append(joinpath(prefix, p))
+            pythonpath.append(joinpath(base_prefix, p))
 
     # Then add stdlib_dir and platstdlib_dir
-    if not stdlib_dir and prefix:
+    if not stdlib_dir and base_prefix:
-        stdlib_dir = joinpath(prefix, STDLIB_SUBDIR)
+        stdlib_dir = joinpath(base_prefix, STDLIB_SUBDIR)
-    if not platstdlib_dir and exec_prefix:
+    if not platstdlib_dir and base_exec_prefix:
-        platstdlib_dir = joinpath(exec_prefix, PLATSTDLIB_LANDMARK)
+        platstdlib_dir = joinpath(base_exec_prefix, PLATSTDLIB_LANDMARK)
 
     if os_name == 'nt':
         # QUIRK: Windows generates paths differently
@@ -750,9 +759,13 @@ elif not pythonpath_was_set:
 
 # QUIRK: Non-Windows replaces prefix/exec_prefix with defaults when running
 # in build directory. This happens after pythonpath calculation.
+# Virtual environments using the build directory Python still keep their prefix.
 if os_name != 'nt' and build_prefix:
+    if not venv_prefix:
         prefix = config.get('prefix') or PREFIX
         exec_prefix = config.get('exec_prefix') or EXEC_PREFIX or prefix
+    base_prefix = config.get('base_prefix') or PREFIX
+    base_exec_prefix = config.get('base_exec_prefix') or EXEC_PREFIX or base_prefix
 
 
 # ******************************************************************************
@@ -788,8 +801,8 @@ config['executable'] = executable
 config['base_executable'] = base_executable
 config['prefix'] = prefix
 config['exec_prefix'] = exec_prefix
-config['base_prefix'] = base_prefix or prefix
+config['base_prefix'] = base_prefix
-config['base_exec_prefix'] = base_exec_prefix or exec_prefix
+config['base_exec_prefix'] = base_exec_prefix
 
 config['platlibdir'] = platlibdir
 # test_embed expects empty strings, not None