Fix couple crashes in dmypy (#18098)

Fixes #18019
Fixes #17775

These two are essentially variations of the same thing. Instead of
adding e.g. `types` to `SENSITIVE_INTERNAL_MODULES` (which would be
fragile and re-introduce same crashes whenever we add a new "core"
module) I add _all stdlib modules_. The only scenario when stdlib
changes is when a version of mypy changes, and in this case the daemon
will be (or should be) restarted anyway.

While adding tests for these I noticed a discrepancy in
`--follow-imports=normal` in the daemon: the files explicitly added on
the command line should be always treated as changed, since otherwise we
will not detect errors if a file was removed from command line in an
intermediate run.

Finally the tests also discovered a spurious error when cache is
disabled (via `/dev/null`).

mypy/build.py

@@ -1050,7 +1050,10 @@ def generate_deps_for_cache(manager: BuildManager, graph: Graph) -> dict[str, di
 def write_plugins_snapshot(manager: BuildManager) -> None:
     """Write snapshot of versions and hashes of currently active plugins."""
     snapshot = json_dumps(manager.plugins_snapshot)
-    if not manager.metastore.write(PLUGIN_SNAPSHOT_FILE, snapshot):
+    if (
+        not manager.metastore.write(PLUGIN_SNAPSHOT_FILE, snapshot)
+        and manager.options.cache_dir != os.devnull
+    ):
         manager.errors.set_file(_cache_dir_prefix(manager.options), None, manager.options)
         manager.errors.report(0, 0, "Error writing plugins snapshot", blocker=True)
 

mypy/dmypy_server.py

@@ -625,6 +625,8 @@ def fine_grained_increment_follow_imports(
         changed, new_files = self.find_reachable_changed_modules(
             sources, graph, seen, changed_paths
         )
+        # Same as in fine_grained_increment().
+        self.add_explicitly_new(sources, changed)
         if explicit_export_types:
             # Same as in fine_grained_increment().
             add_all_sources_to_changed(sources, changed)
@@ -888,6 +890,22 @@ def _find_changed(
             assert path
             removed.append((source.module, path))
 
+        self.add_explicitly_new(sources, changed)
+
+        # Find anything that has had its module path change because of added or removed __init__s
+        last = {s.path: s.module for s in self.previous_sources}
+        for s in sources:
+            assert s.path
+            if s.path in last and last[s.path] != s.module:
+                # Mark it as removed from its old name and changed at its new name
+                removed.append((last[s.path], s.path))
+                changed.append((s.module, s.path))
+
+        return changed, removed
+
+    def add_explicitly_new(
+        self, sources: list[BuildSource], changed: list[tuple[str, str]]
+    ) -> None:
         # Always add modules that were (re-)added, since they may be detected as not changed by
         # fswatcher (if they were actually not changed), but they may still need to be checked
         # in case they had errors before they were deleted from sources on previous runs.
@@ -903,17 +921,6 @@ def _find_changed(
             ]
         )
 
-        # Find anything that has had its module path change because of added or removed __init__s
-        last = {s.path: s.module for s in self.previous_sources}
-        for s in sources:
-            assert s.path
-            if s.path in last and last[s.path] != s.module:
-                # Mark it as removed from its old name and changed at its new name
-                removed.append((last[s.path], s.path))
-                changed.append((s.module, s.path))
-
-        return changed, removed
-
     def cmd_inspect(
         self,
         show: str,

mypy/metastore.py

@@ -27,7 +27,7 @@ class MetadataStore:
 
     @abstractmethod
     def getmtime(self, name: str) -> float:
-        """Read the mtime of a metadata entry..
+        """Read the mtime of a metadata entry.
 
         Raises FileNotFound if the entry does not exist.
         """

mypy/server/update.py

@@ -146,11 +146,7 @@
     TypeInfo,
 )
 from mypy.options import Options
-from mypy.semanal_main import (
-    core_modules,
-    semantic_analysis_for_scc,
-    semantic_analysis_for_targets,
-)
+from mypy.semanal_main import semantic_analysis_for_scc, semantic_analysis_for_targets
 from mypy.server.astdiff import (
     SymbolSnapshot,
     compare_symbol_table_snapshots,
@@ -162,11 +158,12 @@
 from mypy.server.target import trigger_to_target
 from mypy.server.trigger import WILDCARD_TAG, make_trigger
 from mypy.typestate import type_state
-from mypy.util import module_prefix, split_target
+from mypy.util import is_stdlib_file, module_prefix, split_target
 
 MAX_ITER: Final = 1000
 
-SENSITIVE_INTERNAL_MODULES = tuple(core_modules) + ("mypy_extensions", "typing_extensions")
+# These are modules beyond stdlib that have some special meaning for mypy.
+SENSITIVE_INTERNAL_MODULES = ("mypy_extensions", "typing_extensions")
 
 
 class FineGrainedBuildManager:
@@ -406,7 +403,10 @@ def update_module(
         # builtins and friends could potentially get triggered because
         # of protocol stuff, but nothing good could possibly come from
         # actually updating them.
-        if module in SENSITIVE_INTERNAL_MODULES:
+        if (
+            is_stdlib_file(self.manager.options.abs_custom_typeshed_dir, path)
+            or module in SENSITIVE_INTERNAL_MODULES
+        ):
             return [], (module, path), None
 
         manager = self.manager

mypy/util.py

@@ -870,6 +870,18 @@ def is_typeshed_file(typeshed_dir: str | None, file: str) -> bool:
         return False
 
 
+def is_stdlib_file(typeshed_dir: str | None, file: str) -> bool:
+    if "stdlib" not in file:
+        # Fast path
+        return False
+    typeshed_dir = typeshed_dir if typeshed_dir is not None else TYPESHED_DIR
+    stdlib_dir = os.path.join(typeshed_dir, "stdlib")
+    try:
+        return os.path.commonpath((stdlib_dir, os.path.abspath(file))) == stdlib_dir
+    except ValueError:  # Different drives on Windows
+        return False
+
+
 def is_stub_package_file(file: str) -> bool:
     # Use hacky heuristics to check whether file is part of a PEP 561 stub package.
     if not file.endswith(".pyi"):

test-data/unit/daemon.test

@@ -263,6 +263,38 @@ mypy-daemon: error: Missing target module, package, files, or command.
 $ dmypy stop
 Daemon stopped
 
+[case testDaemonRunTwoFilesFullTypeshed]
+$ dmypy run x.py
+Daemon started
+Success: no issues found in 1 source file
+$ dmypy run y.py
+Success: no issues found in 1 source file
+$ dmypy run x.py
+Success: no issues found in 1 source file
+[file x.py]
+[file y.py]
+
+[case testDaemonCheckTwoFilesFullTypeshed]
+$ dmypy start
+Daemon started
+$ dmypy check foo.py
+foo.py:3: error: Incompatible types in assignment (expression has type "str", variable has type "int")  [assignment]
+Found 1 error in 1 file (checked 1 source file)
+== Return code: 1
+$ dmypy check bar.py
+Success: no issues found in 1 source file
+$ dmypy check foo.py
+foo.py:3: error: Incompatible types in assignment (expression has type "str", variable has type "int")  [assignment]
+Found 1 error in 1 file (checked 1 source file)
+== Return code: 1
+[file foo.py]
+from bar import add
+x: str = add("a", "b")
+x_error: int = add("a", "b")
+[file bar.py]
+def add(a, b) -> str:
+    return a + b
+
 [case testDaemonWarningSuccessExitCode-posix]
 $ dmypy run -- foo.py --follow-imports=error --python-version=3.11
 Daemon started