Make per-module ignore_missing_imports work for libs which had bundle…

…d stubs

This makes `ignore_missing_imports` special by making it work a bit
differently, depending on whether it's set globally or per module.

The new behavior is less surprising. This makes it possible to ignore
arbitrary missing third-party stub packages, even those which used to
have bundled stubs.

Fixes #10283.

mypy/build.py

@@ -2448,7 +2448,9 @@ def find_module_and_diagnose(manager: BuildManager,
         # otherwise updating mypy can silently result in new false
         # negatives.
         global_ignore_missing_imports = manager.options.ignore_missing_imports
-        if top_level in legacy_bundled_packages and global_ignore_missing_imports:
+        if (top_level in legacy_bundled_packages
+                and global_ignore_missing_imports
+                and not options.ignore_missing_imports_per_module):
             ignore_missing_imports = False
 
         if skip_diagnose:

mypy/options.py

@@ -82,6 +82,8 @@ def __init__(self) -> None:
         self.no_silence_site_packages = False
         self.no_site_packages = False
         self.ignore_missing_imports = False
+        # Is ignore_missing_imports set in a per-module section
+        self.ignore_missing_imports_per_module = False
         self.follow_imports = 'normal'  # normal|silent|skip|error
         # Whether to respect the follow_imports setting even for stub files.
         # Intended to be used for disabling specific stubs.
@@ -321,6 +323,10 @@ def apply_changes(self, changes: Dict[str, object]) -> 'Options':
         replace_object_state(new_options, self, copy_dict=True)
         for key, value in changes.items():
             setattr(new_options, key, value)
+        if changes.get("ignore_missing_imports"):
+            # This is the only option for which a per-module and a global
+            # option sometimes beheave differently.
+            new_options.ignore_missing_imports_per_module = True
         return new_options
 
     def build_per_module_cache(self) -> None:

test-data/unit/check-modules.test

@@ -2982,3 +2982,34 @@ T = TypeVar("T")
 class F(M):
     x: C
     class C: ...
+
+[case testIgnoreErrorFromMissingStubs1]
+# flags: --config-file tmp/pyproject.toml
+import certifi
+from foobar1 import x
+import foobar2
+[file pyproject.toml]
+\[tool.mypy]
+ignore_missing_imports = true
+\[[tool.mypy.overrides]]
+module = "certifi"
+ignore_missing_imports = true
+\[[tool.mypy.overrides]]
+module = "foobar1"
+ignore_missing_imports = true
+
+[case testIgnoreErrorFromMissingStubs2]
+# flags: --config-file tmp/pyproject.toml
+import certifi
+from foobar1 import x
+import foobar2  # E: Cannot find implementation or library stub for module named "foobar2" \
+                # N: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
+[file pyproject.toml]
+\[tool.mypy]
+ignore_missing_imports = false
+\[[tool.mypy.overrides]]
+module = "certifi"
+ignore_missing_imports = true
+\[[tool.mypy.overrides]]
+module = "foobar1"
+ignore_missing_imports = true