Fix daemon crash caused by deleted submodule

If a submodule has been deleted while using a fine-grained cache,
the daemon could crash during fixup, since there could be a
symbol table entry in a parent package that would appear to
refer to itself. Handle the case by adding a placeholder symbol
table entry instead. Eventually the parent package will be
reprocessed and the symbol table will be completed.

mypy/fixup.py

@@ -128,8 +128,23 @@ def visit_symbol_table(self, symtab: SymbolTable, table_fullname: str) -> None:
                         cross_ref, self.modules, raise_on_missing=not self.allow_missing
                     )
                     if stnode is not None:
-                        assert stnode.node is not None, (table_fullname + "." + key, cross_ref)
-                        value.node = stnode.node
+                        if stnode is value:
+                            # The node seems to refer to itself, which can mean that
+                            # the target is a deleted submodule of the current module,
+                            # and thus lookup falls back to the symbol table of the parent
+                            # package. Here's how this may happen:
+                            #
+                            #   pkg/__init__.py:
+                            #     from pkg import sub
+                            #
+                            # Now if pkg.sub is deleted, the pkg.sub symbol table entry
+                            # appears to refer to itself. Replace the entry with a
+                            # placeholder to avoid a crash. We can't delete the entry,
+                            # as it would stop dependency propagation.
+                            value.node = Var(key + "@deleted")
+                        else:
+                            assert stnode.node is not None, (table_fullname + "." + key, cross_ref)
+                            value.node = stnode.node
                     elif not self.allow_missing:
                         assert False, f"Could not find cross-ref {cross_ref}"
                     else:

mypy/nodes.py

@@ -3824,6 +3824,8 @@ def __str__(self) -> str:
         # Include declared type of variables and functions.
         if self.type is not None:
             s += f" : {self.type}"
+        if self.cross_ref:
+            s += f" cross_ref:{self.cross_ref}"
         return s
 
     def serialize(self, prefix: str, name: str) -> JsonDict:

test-data/unit/fine-grained.test

@@ -10486,3 +10486,22 @@ reveal_type(s)
 ==
 ==
 b.py:2: note: Revealed type is "builtins.str"
+
+[case testRenameSubModule]
+import a
+
+[file a.py]
+import pkg.sub
+
+[file pkg/__init__.py]
+[file pkg/sub/__init__.py]
+from pkg.sub import mod
+[file pkg/sub/mod.py]
+
+[file pkg/sub/__init__.py.2]
+from pkg.sub import modb
+[delete pkg/sub/mod.py.2]
+[file pkg/sub/modb.py.2]
+
+[out]
+==