Refine the implementation of site configuration for virtual environme…

…nts.

src/pip/_internal/configuration.py

@@ -75,13 +75,13 @@ def get_configuration_files():
         for path in appdirs.site_config_dirs('pip')
     ]
 
-    site_config_files = [
-        os.path.join(sys.prefix, CONFIG_BASENAME)
-    ]
+    site_config_files = []
     if getattr(sys, 'base_prefix', sys.prefix) != sys.prefix:
         site_config_files.append(
             os.path.join(sys.base_prefix, CONFIG_BASENAME),
         )
+    # A virtual environment config takes precedence over a base_prefix config.
+    site_config_files.append(os.path.join(sys.prefix, CONFIG_BASENAME))
 
     legacy_config_file = os.path.join(
         os.path.expanduser('~'),

tests/unit/test_configuration.py

@@ -189,10 +189,11 @@ def test_site_modification(self):
 
         self.configuration.set_value("test.hello", "10")
 
-        # get the path to site config file
+        # get the path to site config file, mirroring the behaviour
+        # in _get_parser_to_modify.
         assert mymock.call_count == 1
         assert mymock.call_args[0][0] == (
-            get_configuration_files()[kinds.SITE][0]
+            get_configuration_files()[kinds.SITE][-1]
         )
 
     def test_user_modification(self):

tests/unit/test_options.py

@@ -1,5 +1,6 @@
 import os
 from contextlib import contextmanager
+import sys
 from tempfile import NamedTemporaryFile
 
 import pytest
@@ -433,20 +434,29 @@ def test_client_cert(self):
 
 class TestOptionsConfigFiles:
 
-    def test_venv_config_file_found(self, monkeypatch):
+    @pytest.mark.parametrize("in_venv", (True, False))
+    def test_venv_config_file_found(self, monkeypatch, in_venv):
         # strict limit on the global config files list
         monkeypatch.setattr(
             pip._internal.utils.appdirs, 'site_config_dirs',
             lambda _: ['/a/place']
         )
+        if in_venv:
+            monkeypatch.setattr(sys, 'base_prefix', '/some/other/place')
+        else:
+            monkeypatch.setattr(sys, 'base_prefix', sys.prefix)
 
         cp = pip._internal.configuration.Configuration(isolated=False)
 
         files = []
         for _, val in cp.iter_config_files():
             files.extend(val)
 
-        assert len(files) == 4
+        if in_venv:
+            # With venvs we get the config from the base_prefix also.
+            assert len(files) == 5
+        else:
+            assert len(files) == 4
 
     @pytest.mark.parametrize(
         "args, expect",