Add extra check to filter out non-modules

This commit adds an (ad-hoc) check to the indirect dependencies patcher
to filter out computed dependencies that are not, in fact, actually
modules. Ideally, this ad-hoc check shouldn't be necessary but there are
enough weird edge cases that it seems like a useful thing to have to
prevent unexpected behavior.

Author: MichaelLeeDBX

mypy/build.py

@@ -1436,6 +1436,8 @@ def _patch_indirect_dependencies(self, module_refs: Set[str]) -> None:
         extra = encountered - valid
 
         for dep in sorted(extra):
+            if dep not in self.manager.modules:
+                continue
             if dep not in self.suppressed and dep not in self.manager.missing_modules:
                 self.dependencies.append(dep)
                 self.priorities[dep] = PRI_INDIRECT