Type ignore comments erroneously marked as unused by dmypy

mypy/dmypy_server.py

@@ -684,10 +684,11 @@ def refresh_file(module: str, path: str) -> list[str]:
 
         # Find all original modules in graph that were not reached -- they are deleted.
         to_delete = []
+        seen_and_ancestors = self._seen_and_ancestors(seen)
         for module_id in orig_modules:
             if module_id not in graph:
                 continue
-            if module_id not in seen:
+            if module_id not in seen_and_ancestors:
                 module_path = graph[module_id].path
                 assert module_path is not None
                 to_delete.append((module_id, module_path))
@@ -715,6 +716,29 @@ def refresh_file(module: str, path: str) -> list[str]:
 
         return messages
 
+    def _seen_and_ancestors(self, seen: set[str]) -> set[str]:
+        """Return the set of seen modules along with any ancestors not already in the set.
+
+        For example, given this set:
+
+            {"foo", "foo.bar", "a.b.c"}
+
+        ... we would expect this set to be returned:
+
+            {"foo", "foo.bar", "a.b.c", "a.b", "a"}
+
+        This is used to stop us from deleting ancestor modules from the graph
+        when their descendants have been seen.
+        """
+        seen_paths = seen.copy()
+        for module_path in seen:
+            while module_path := module_path.rpartition(".")[0]:
+                if module_path in seen_paths:
+                    break
+                else:
+                    seen_paths.add(module_path)
+        return seen_paths
+
     def find_reachable_changed_modules(
         self,
         roots: list[BuildSource],

mypy/errors.py

@@ -725,6 +725,8 @@ def generate_unused_ignore_errors(self, file: str) -> None:
                 blocker=False,
                 only_once=False,
                 allow_dups=False,
+                origin=(self.file, [line]),
+                target=self.target_module,
             )
             self._add_error_info(file, info)
 
@@ -777,6 +779,8 @@ def generate_ignore_without_code_errors(
                 blocker=False,
                 only_once=False,
                 allow_dups=False,
+                origin=(self.file, [line]),
+                target=self.target_module,
             )
             self._add_error_info(file, info)
 

mypy/server/update.py

@@ -667,6 +667,8 @@ def restore(ids: list[str]) -> None:
     state.type_check_first_pass()
     state.type_check_second_pass()
     state.detect_possibly_undefined_vars()
+    state.generate_unused_ignore_notes()
+    state.generate_ignore_without_code_notes()
     t2 = time.time()
     state.finish_passes()
     t3 = time.time()
@@ -1028,6 +1030,10 @@ def key(node: FineGrainedDeferredNode) -> int:
         if graph[module_id].type_checker().check_second_pass():
             more = True
 
+    graph[module_id].detect_possibly_undefined_vars()
+    graph[module_id].generate_unused_ignore_notes()
+    graph[module_id].generate_ignore_without_code_notes()
+
     if manager.options.export_types:
         manager.all_types.update(graph[module_id].type_map())
 

test-data/unit/daemon.test

@@ -615,3 +615,140 @@ b: str
 from demo.test import a
 [file demo/test.py]
 a: int
+
+[case testUnusedTypeIgnorePreservedOnRerun]
+-- Regression test for https://github.com/python/mypy/issues/9655
+$ dmypy start -- --warn-unused-ignores --no-error-summary --hide-error-codes
+Daemon started
+$ dmypy check -- bar.py
+bar.py:2: error: Unused "type: ignore" comment
+== Return code: 1
+$ dmypy check -- bar.py
+bar.py:2: error: Unused "type: ignore" comment
+== Return code: 1
+
+[file foo/__init__.py]
+[file foo/empty.py]
+[file bar.py]
+from foo.empty import *
+a = 1  # type: ignore
+
+[case testTypeIgnoreWithoutCodePreservedOnRerun]
+-- Regression test for https://github.com/python/mypy/issues/9655
+$ dmypy start -- --enable-error-code ignore-without-code --no-error-summary
+Daemon started
+$ dmypy check -- bar.py
+bar.py:2: error: "type: ignore" comment without error code  [ignore-without-code]
+== Return code: 1
+$ dmypy check -- bar.py
+bar.py:2: error: "type: ignore" comment without error code  [ignore-without-code]
+== Return code: 1
+
+[file foo/__init__.py]
+[file foo/empty.py]
+[file bar.py]
+from foo.empty import *
+a = 1  # type: ignore
+
+[case testPossiblyUndefinedVarsPreservedAfterRerun]
+-- Regression test for https://github.com/python/mypy/issues/9655
+$ dmypy start -- --enable-error-code possibly-undefined --no-error-summary
+Daemon started
+$ dmypy check -- bar.py
+bar.py:4: error: Name "a" may be undefined  [possibly-undefined]
+== Return code: 1
+$ dmypy check -- bar.py
+bar.py:4: error: Name "a" may be undefined  [possibly-undefined]
+== Return code: 1
+
+[file foo/__init__.py]
+[file foo/empty.py]
+[file bar.py]
+from foo.empty import *
+if False:
+    a = 1
+a
+
+[case testUnusedTypeIgnorePreservedOnRerunWithIgnoredMissingImports]
+$ dmypy start -- --no-error-summary --ignore-missing-imports --warn-unused-ignores
+Daemon started
+$ dmypy check foo
+foo/main.py:3: error: Unused "type: ignore" comment  [unused-ignore]
+== Return code: 1
+$ dmypy check foo
+foo/main.py:3: error: Unused "type: ignore" comment  [unused-ignore]
+== Return code: 1
+
+[file unused/__init__.py]
+[file unused/submodule.py]
+[file foo/empty.py]
+[file foo/__init__.py]
+from foo.main import *
+from unused.submodule import *
+[file foo/main.py]
+from foo import empty
+from foo.does_not_exist import *
+a = 1  # type: ignore
+
+[case testModuleDoesNotExistPreservedOnRerun]
+$ dmypy start -- --no-error-summary --ignore-missing-imports
+Daemon started
+$ dmypy check foo
+foo/main.py:1: error: Module "foo" has no attribute "does_not_exist"  [attr-defined]
+== Return code: 1
+$ dmypy check foo
+foo/main.py:1: error: Module "foo" has no attribute "does_not_exist"  [attr-defined]
+== Return code: 1
+
+[file unused/__init__.py]
+[file unused/submodule.py]
+[file foo/__init__.py]
+from foo.main import *
+[file foo/main.py]
+from foo import does_not_exist
+from unused.submodule import *
+
+[case testReturnTypeIgnoreAfterUnknownImport]
+-- Return type ignores after unknown imports and unused modules are respected on the second pass.
+$ dmypy start -- --warn-unused-ignores --no-error-summary
+Daemon started
+$ dmypy check -- foo.py
+foo.py:2: error: Cannot find implementation or library stub for module named "a_module_which_does_not_exist"  [import-not-found]
+foo.py:2: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
+== Return code: 1
+$ dmypy check -- foo.py
+foo.py:2: error: Cannot find implementation or library stub for module named "a_module_which_does_not_exist"  [import-not-found]
+foo.py:2: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
+== Return code: 1
+
+[file unused/__init__.py]
+[file unused/empty.py]
+[file foo.py]
+from unused.empty import *
+import a_module_which_does_not_exist
+def is_foo() -> str:
+    return True  # type: ignore
+
+[case testAttrsTypeIgnoreAfterUnknownImport]
+$ dmypy start -- --warn-unused-ignores --no-error-summary
+Daemon started
+$ dmypy check -- foo.py
+foo.py:3: error: Cannot find implementation or library stub for module named "a_module_which_does_not_exist"  [import-not-found]
+foo.py:3: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
+== Return code: 1
+$ dmypy check -- foo.py
+foo.py:3: error: Cannot find implementation or library stub for module named "a_module_which_does_not_exist"  [import-not-found]
+foo.py:3: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
+== Return code: 1
+
+[file unused/__init__.py]
+[file unused/empty.py]
+[file foo.py]
+import attr
+from unused.empty import *
+import a_module_which_does_not_exist
+
+@attr.frozen
+class A:
+    def __init__(self) -> None:
+        self.__attrs_init__()  # type: ignore[attr-defined]

test-data/unit/fine-grained.test

@@ -10505,3 +10505,27 @@ from pkg.sub import modb
 
 [out]
 ==
+
+[case testUnusedTypeIgnorePreservedAfterChange]
+# flags: --warn-unused-ignores --no-error-summary
+[file main.py]
+a = 1  # type: ignore
+[file main.py.2]
+a = 1  # type: ignore
+# Comment to trigger reload.
+[out]
+main.py:1: error: Unused "type: ignore" comment
+==
+main.py:1: error: Unused "type: ignore" comment
+
+[case testTypeIgnoreWithoutCodePreservedAfterChange]
+# flags: --enable-error-code ignore-without-code --no-error-summary
+[file main.py]
+a = 1  # type: ignore
+[file main.py.2]
+a = 1  # type: ignore
+# Comment to trigger reload.
+[out]
+main.py:1: error: "type: ignore" comment without error code
+==
+main.py:1: error: "type: ignore" comment without error code