Fix from p import q when p/q.py removed from fine-grained build (#4988)

Author: msullivan

mypy/server/update.py

@@ -461,7 +461,7 @@ def update_module_isolated(module: str,
         manager.log_fine_grained('new module %r' % module)
 
     if not manager.fscache.isfile(path) or force_removed:
-        delete_module(module, graph, manager)
+        delete_module(module, path, graph, manager)
         return NormalUpdate(module, path, [], None)
 
     sources = get_sources(manager.fscache, previous_modules, [(module, path)])
@@ -579,6 +579,7 @@ def find_relative_leaf_module(modules: List[Tuple[str, str]], graph: Graph) -> T
 
 
 def delete_module(module_id: str,
+                  path: str,
                   graph: Graph,
                   manager: BuildManager) -> None:
     manager.log_fine_grained('delete module %r' % module_id)
@@ -596,6 +597,10 @@ def delete_module(module_id: str,
             parent = manager.modules[parent_id]
             if components[-1] in parent.names:
                 del parent.names[components[-1]]
+    # If the module is removed from the build but still exists, then
+    # we mark it as missing so that it will get picked up by import from still.
+    if manager.fscache.isfile(path):
+        manager.missing_modules.add(module_id)
 
 
 def dedupe_modules(modules: List[Tuple[str, str]]) -> List[Tuple[str, str]]:

test-data/unit/fine-grained-modules.test

@@ -134,6 +134,25 @@ b.py:1: error: Name 'f' is not defined
 ==
 b.py:1: error: Name 'f' is not defined
 
+[case testRemoveSubmoduleFromBuild1]
+# cmd1: mypy a.py b/__init__.py b/c.py
+# cmd2: mypy a.py b/__init__.py
+# flags: --follow-imports=skip --ignore-missing-imports
+[file a.py]
+from b import c
+x=1
+[file a.py.2]
+from b import c
+x=2
+[file a.py.3]
+from b import c
+x=3
+[file b/__init__.py]
+[file b/c.py]
+[out]
+==
+==
+
 [case testImportLineNumber1]
 import b
 [file b.py]