[stubtest] fix duplicate errors with invalid line numbers (#20417)

Closes #15023

Author: jorenham

mypy/stubtest.py

@@ -424,6 +424,18 @@ def _belongs_to_runtime(r: types.ModuleType, attr: str) -> bool:
 
     for entry in sorted(to_check):
         stub_entry = stub.names[entry].node if entry in stub.names else MISSING
+        if entry in stub.names:
+            if xref := stub.names[entry].cross_ref:
+                orig_module = xref.rsplit(".", 1)[0]
+            elif isinstance(stub_entry, nodes.SymbolNode) and (name := stub_entry.fullname):
+                orig_module = name.rsplit(".", 1)[0]
+            else:
+                orig_module = None
+
+            if orig_module and orig_module != stub.fullname and orig_module in _all_stubs:
+                # Skip re-exported names whose defining module will be checked separately.
+                continue
+
         if isinstance(stub_entry, nodes.MypyFile):
             # Don't recursively check exported modules, since that leads to infinite recursion
             continue

mypy/test/teststubtest.py

@@ -10,6 +10,7 @@
 import textwrap
 import unittest
 from collections.abc import Callable, Iterator
+from pathlib import Path
 from typing import Any
 
 from pytest import raises
@@ -2748,6 +2749,33 @@ def test_output(self) -> None:
         )
         assert output == expected
 
+    def test_reexport_reports_import_location(self) -> None:
+        with use_tmp_dir(TEST_MODULE_NAME) as tmp_dir:
+            Path("builtins.pyi").write_text(stubtest_builtins_stub)
+            Path("typing.pyi").write_text(stubtest_typing_stub)
+            Path("enum.pyi").write_text(stubtest_enum_stub)
+
+            os.makedirs("test_module", exist_ok=True)
+            Path("test_module/__init__.pyi").write_text("from .mod import f")
+            Path("test_module/__init__.py").write_text("from .mod import f")
+            Path("test_module/mod.pyi").write_text("def f(self) -> None: ...")
+            Path("test_module/mod.py").write_text("def f(self, x): pass")
+
+            output = io.StringIO()
+            outerr = io.StringIO()
+            with contextlib.redirect_stdout(output), contextlib.redirect_stderr(outerr):
+                test_stubs(parse_options([TEST_MODULE_NAME]), use_builtins_fixtures=True)
+
+            filtered_output = remove_color_code(
+                output.getvalue()
+                .replace(os.path.realpath(tmp_dir) + os.sep, "")
+                .replace(tmp_dir + os.sep, "")
+            )
+
+        assert filtered_output.count('stub does not have parameter "x"') == 1
+        assert "__init__.pyi" not in filtered_output
+        assert "mod.py:1" in filtered_output
+
     def test_ignore_flags(self) -> None:
         output = run_stubtest(
             stub="", runtime="__all__ = ['f']\ndef f(): pass", options=["--ignore-missing-stub"]