Address #3796 and add a test for it.

src/_pytest/python.py

@@ -597,14 +597,16 @@ class Package(Module):
             if path.basename == "__init__.py" and path.dirpath() == this_path:
                 continue
 
+            for pkg_prefix in pkg_prefixes:
+                if pkg_prefix in path.parts() and pkg_prefix.join('__init__.py') != path:
+                    skip = True
+
+            if skip:
+                continue
+
             if path.isdir() and path.join('__init__.py').check(file=1):
                 pkg_prefixes.add(path)
 
-            for pkg_prefix in pkg_prefixes:
-                if pkg_prefix in path.parts() and pkg_prefix.join('__init__.py') == path:
-                    skip = True
-            if skip:
-                continue
             for x in self._collectfile(path):
                 yield x
 

testing/python/fixture.py

@@ -3979,3 +3979,71 @@ class TestScopeOrdering(object):
         items, _ = testdir.inline_genitems()
         request = FixtureRequest(items[0])
         assert request.fixturenames == "s1 p1 m1 m2 c1 f2 f1".split()
+
+    def test_multiple_packages(self, testdir):
+        """Complex test involving multiple package fixtures. Make sure teardowns
+        are executed in order.
+        .
+        └── root
+            ├── __init__.py
+            ├── sub1
+            │   ├── __init__.py
+            │   ├── conftest.py
+            │   └── test_1.py
+            └── sub2
+                ├── __init__.py
+                ├── conftest.py
+                └── test_2.py
+        """
+        root = testdir.mkdir("root")
+        root.join("__init__.py").write("values = []")
+        sub1 = root.mkdir("sub1")
+        sub1.ensure("__init__.py")
+        sub1.join("conftest.py").write(
+            dedent(
+                """\
+            import pytest
+            from .. import values
+            @pytest.fixture(scope="package")
+            def fix():
+                values.append("pre-sub1")
+                yield values
+                values.pop()
+        """
+            )
+        )
+        sub1.join("test_1.py").write(
+            dedent(
+                """\
+            from .. import values
+            def test_1(fix):
+                assert values == ["pre-sub1"]
+        """
+            )
+        )
+        sub2 = root.mkdir("sub2")
+        sub2.ensure("__init__.py")
+        sub2.join("conftest.py").write(
+            dedent(
+                """\
+            import pytest
+            from .. import values
+            @pytest.fixture(scope="package")
+            def fix():
+                values.append("pre-sub2")
+                yield values
+                values.pop()
+        """
+            )
+        )
+        sub2.join("test_2.py").write(
+            dedent(
+                """\
+            from .. import values
+            def test_2(fix):
+                assert values == ["pre-sub2"]
+        """
+            )
+        )
+        reprec = testdir.inline_run()
+        reprec.assertoutcome(passed=2)