Invalidate cache when previously missing stubs are added (#5465)

Fixes #1910
Fixes #5101

Author: ilevkivskyi

mypy/build.py

@@ -1884,6 +1884,25 @@ def __init__(self,
             self.child_modules = set(self.meta.child_modules)
             if temporary:
                 self.load_tree(temporary=True)
+            if not manager.use_fine_grained_cache():
+                # Special case: if there were a previously missing package imported here
+                # and it is not present, then we need to re-calculate dependencies.
+                # This is to support patterns like this:
+                #     from missing_package import missing_module  # type: ignore
+                # At first mypy doesn't know that `missing_module` is a module
+                # (it may be a variable, a class, or a function), so it is not added to
+                # suppressed dependencies. Therefore, when the package with module is added,
+                # we need to re-calculate dependencies.
+                # NOTE: see comment below for why we skip this in fine grained mode.
+                new_packages = False
+                for dep in self.suppressed:
+                    path = manager.find_module_cache.find_module(dep, manager.search_paths,
+                                                              manager.options.python_executable)
+                    if path and '__init__.py' in path:
+                        new_packages = True
+                if new_packages:
+                    self.parse_file()  # This is safe because the cache is anyway stale.
+                    self.compute_dependencies()
         else:
             # When doing a fine-grained cache load, pretend we only
             # know about modules that have cache information and defer
@@ -2696,12 +2715,15 @@ def load_graph(sources: List[BuildSource], manager: BuildManager,
         #   (since direct dependencies reflect the imports found in the source)
         #   but A's cached *indirect* dependency on C is wrong.
         dependencies = [dep for dep in st.dependencies if st.priorities.get(dep) != PRI_INDIRECT]
+        added = [dep for dep in st.suppressed
+                 if manager.find_module_cache.find_module(dep, manager.search_paths,
+                                                          manager.options.python_executable)]
         for dep in st.ancestors + dependencies + st.suppressed:
             # We don't want to recheck imports marked with '# type: ignore'
             # so we ignore any suppressed module not explicitly re-included
             # from the command line.
             ignored = dep in st.suppressed and dep not in entry_points
-            if ignored:
+            if ignored and dep not in added:
                 manager.missing_modules.add(dep)
             elif dep not in graph:
                 try:

test-data/unit/check-incremental.test

@@ -4790,3 +4790,97 @@ tmp/c.py:1: note: (Perhaps setting MYPYPATH or using the "--ignore-missing-impor
 [out2]
 tmp/c.py:1: error: Cannot find module named 'a.b.c'
 tmp/c.py:1: note: (Perhaps setting MYPYPATH or using the "--ignore-missing-imports" flag would help)
+
+[case testAddedMissingStubs]
+# flags: --ignore-missing-imports
+from missing import f
+f(int())
+[file missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:3: error: Argument 1 to "f" has incompatible type "int"; expected "str"
+
+[case testAddedMissingStubsPackage]
+# flags: --ignore-missing-imports
+import package.missing
+package.missing.f(int())
+[file package/__init__.pyi.2]
+[file package/missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:3: error: Argument 1 to "f" has incompatible type "int"; expected "str"
+
+[case testAddedMissingStubsPackageFrom]
+# flags: --ignore-missing-imports
+from package import missing
+missing.f(int())
+[file package/__init__.pyi.2]
+[file package/missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:3: error: Argument 1 to "f" has incompatible type "int"; expected "str"
+
+[case testAddedMissingStubsPackagePartial]
+# flags: --ignore-missing-imports
+import package.missing
+package.missing.f(int())
+[file package/__init__.pyi]
+[file package/missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:3: error: Argument 1 to "f" has incompatible type "int"; expected "str"
+
+[case testAddedMissingStubsPackagePartialGetAttr]
+import package.missing
+package.missing.f(int())
+[file package/__init__.pyi]
+from typing import Any
+def __getattr__(attr: str) -> Any: ...
+[file package/missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:2: error: Argument 1 to "f" has incompatible type "int"; expected "str"
+
+[case testAddedMissingStubsIgnore]
+from missing import f  # type: ignore
+f(int())
+[file missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:2: error: Argument 1 to "f" has incompatible type "int"; expected "str"
+
+[case testAddedMissingStubsIgnorePackage]
+import package.missing  # type: ignore
+package.missing.f(int())
+[file package/__init__.pyi.2]
+[file package/missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:2: error: Argument 1 to "f" has incompatible type "int"; expected "str"
+
+[case testAddedMissingStubsIgnorePackageFrom]
+from package import missing  # type: ignore
+missing.f(int())
+[file package/__init__.pyi.2]
+[file package/missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:2: error: Argument 1 to "f" has incompatible type "int"; expected "str"
+
+[case testAddedMissingStubsIgnorePackagePartial]
+import package.missing  # type: ignore
+package.missing.f(int())
+[file package/__init__.pyi]
+[file package/missing.pyi.2]
+def f(x: str) -> None: pass
+[out]
+[out2]
+main:2: error: Argument 1 to "f" has incompatible type "int"; expected "str"