Optimize fine-grained update by using Graph as the cache (python#4622)

Make fine-grained update use a Graph as the source of truth instead of a SavedCache. We modify load_graph to optionally use an existing graph as a starting point. This allows us to skip the expensive full load_graph and preserve_full_cache operations that essentially only convert between Graph and SavedCache.

This requires a nontrivial change to the loading of dependency information in build.
Since we are no longer doing a full `load_graph()`, we can't rely on
it fully populating `missing_modules` if it is cleared between
updates. If `missing_modules` isn't fully populated, then semanal will
spuriously reject `from x import y` where `x.y` is a missing module.

We can't just *not* clear `missing_modules`, however, because
`parse_file` uses it to decide that modules are suppressed. But this
is actually wrong! It can lead to an import failure message not being
generated because some other module has already failed to import it
(and perhaps even ignored the error).

`parse_file()` shouldn't actually *need* to compute `suppressed`,
though. If it is called on a file with no cache, `load_graph()` will
handle moving deps to `suppressed`, and if called on a file that has
had cache info loaded, then the dependency information has all been
loaded from the cache.

So we refactor things so that dep information from the cache is used
when available and `parse_file` doesn't need to deal with it.

I strongly suspect that this refactor obviates the need for
`fix_suppressed_dependencies`, but I was not able to quickly produce a
test case from the description in python#2036, so I am not comfortable
making that change.

mypy/build.py

@@ -389,7 +389,6 @@ def default_lib_path(data_dir: str,
 CacheMeta = NamedTuple('CacheMeta',
                        [('id', str),
                         ('path', str),
-                        ('memory_only', bool),  # no corresponding json files (fine-grained only)
                         ('mtime', int),
                         ('size', int),
                         ('hash', str),
@@ -415,7 +414,6 @@ def cache_meta_from_dict(meta: Dict[str, Any], data_json: str) -> CacheMeta:
     return CacheMeta(
         meta.get('id', sentinel),
         meta.get('path', sentinel),
-        meta.get('memory_only', False),
         int(meta['mtime']) if 'mtime' in meta else sentinel,
         meta.get('size', sentinel),
         meta.get('hash', sentinel),
@@ -569,7 +567,7 @@ class BuildManager:
       plugin:          Active mypy plugin(s)
       errors:          Used for reporting all errors
       flush_errors:    A function for processing errors after each SCC
-      saved_cache:     Dict with saved cache state for dmypy and fine-grained incremental mode
+      saved_cache:     Dict with saved cache state for coarse-grained dmypy
                        (read-write!)
       stats:           Dict with various instrumentation numbers
     """
@@ -626,6 +624,8 @@ def all_imported_modules_in_file(self,
 
         Return list of tuples (priority, module id, import line number)
         for all modules imported in file; lower numbers == higher priority.
+
+        Can generate blocking errors on bogus relative imports.
         """
 
         def correct_rel_imp(imp: Union[ImportFrom, ImportAll]) -> str:
@@ -640,6 +640,12 @@ def correct_rel_imp(imp: Union[ImportFrom, ImportAll]) -> str:
                 file_id = ".".join(file_id.split(".")[:-rel])
             new_id = file_id + "." + imp.id if imp.id else file_id
 
+            if not new_id:
+                self.errors.set_file(file.path, file.name())
+                self.errors.report(imp.line, 0,
+                                   "No parent module -- cannot perform relative import",
+                                   blocker=True)
+
             return new_id
 
         res = []  # type: List[Tuple[int, str, int]]
@@ -1129,12 +1135,6 @@ def validate_meta(meta: Optional[CacheMeta], id: str, path: Optional[str],
         manager.log('Metadata abandoned for {}: errors were previously ignored'.format(id))
         return None
 
-    if meta.memory_only:
-        # Special case for fine-grained incremental mode when the JSON file is missing but
-        # we want to cache the module anyway.
-        manager.log('Memory-only metadata for {}'.format(id))
-        return meta
-
     assert path is not None, "Internal error: meta was provided without a path"
     # Check data_json; assume if its mtime matches it's good.
     # TODO: stat() errors
@@ -1626,7 +1626,8 @@ def __init__(self,
                         self.ignore_all = True
                     else:
                         # In 'error' mode, produce special error messages.
-                        manager.log("Skipping %s (%s)" % (path, id))
+                        if id not in manager.missing_modules:
+                            manager.log("Skipping %s (%s)" % (path, id))
                         if follow_imports == 'error':
                             if ancestor_for:
                                 self.skipping_ancestor(id, path, ancestor_for)
@@ -1678,7 +1679,7 @@ def __init__(self,
         else:
             # Parse the file (and then some) to get the dependencies.
             self.parse_file()
-            self.suppressed = []
+            self.compute_dependencies()
             self.child_modules = set()
 
     def skipping_ancestor(self, id: str, path: str, ancestor_for: 'State') -> None:
@@ -1833,6 +1834,8 @@ def fix_suppressed_dependencies(self, graph: Graph) -> None:
         """
         # TODO: See if it's possible to move this check directly into parse_file in some way.
         # TODO: Find a way to write a test case for this fix.
+        # TODO: I suspect that splitting compute_dependencies() out from parse_file
+        # obviates the need for this but lacking a test case for the problem this fixed...
         silent_mode = (self.options.ignore_missing_imports or
                        self.options.follow_imports == 'skip')
         if not silent_mode:
@@ -1899,49 +1902,48 @@ def parse_file(self) -> None:
         # TODO: Why can't SemanticAnalyzerPass1 .analyze() do this?
         self.tree.names = manager.semantic_analyzer.globals
 
+        self.check_blockers()
+
+    def compute_dependencies(self) -> None:
+        """Compute a module's dependencies after parsing it.
+
+        This is used when we parse a file that we didn't have
+        up-to-date cache information for. When we have an up-to-date
+        cache, we just use the cached info.
+        """
+        manager = self.manager
+        assert self.tree is not None
+
         # Compute (direct) dependencies.
         # Add all direct imports (this is why we needed the first pass).
         # Also keep track of each dependency's source line.
         dependencies = []
-        suppressed = []
         priorities = {}  # type: Dict[str, int]  # id -> priority
         dep_line_map = {}  # type: Dict[str, int]  # id -> line
         for pri, id, line in manager.all_imported_modules_in_file(self.tree):
             priorities[id] = min(pri, priorities.get(id, PRI_ALL))
             if id == self.id:
                 continue
-            # Omit missing modules, as otherwise we could not type-check
-            # programs with missing modules.
-            if id in manager.missing_modules:
-                if id not in dep_line_map:
-                    suppressed.append(id)
-                    dep_line_map[id] = line
-                continue
-            if id == '':
-                # Must be from a relative import.
-                manager.errors.set_file(self.xpath, self.id)
-                manager.errors.report(line, 0,
-                                      "No parent module -- cannot perform relative import",
-                                      blocker=True)
-                continue
             if id not in dep_line_map:
                 dependencies.append(id)
                 dep_line_map[id] = line
         # Every module implicitly depends on builtins.
         if self.id != 'builtins' and 'builtins' not in dep_line_map:
             dependencies.append('builtins')
 
-        # If self.dependencies is already set, it was read from the
-        # cache, but for some reason we're re-parsing the file.
         # NOTE: What to do about race conditions (like editing the
         # file while mypy runs)?  A previous version of this code
         # explicitly checked for this, but ran afoul of other reasons
         # for differences (e.g. silent mode).
+
+        # Missing dependencies will be moved from dependencies to
+        # suppressed when they fail to be loaded in load_graph.
         self.dependencies = dependencies
-        self.suppressed = suppressed
+        self.suppressed = []
         self.priorities = priorities
         self.dep_line_map = dep_line_map
-        self.check_blockers()
+
+        self.check_blockers()  # Can fail due to bogus relative imports
 
     def semantic_analysis(self) -> None:
         assert self.tree is not None, "Internal error: method must be called on parsed file only"
@@ -2198,13 +2200,19 @@ def dump_graph(graph: Graph) -> None:
     print("[" + ",\n ".join(node.dumps() for node in nodes) + "\n]")
 
 
-def load_graph(sources: List[BuildSource], manager: BuildManager) -> Graph:
+def load_graph(sources: List[BuildSource], manager: BuildManager,
+               old_graph: Optional[Graph] = None) -> Graph:
     """Given some source files, load the full dependency graph.
 
+    If an old_graph is passed in, it is used as the starting point and
+    modified during graph loading.
+
     As this may need to parse files, this can raise CompileError in case
     there are syntax errors.
     """
-    graph = {}  # type: Graph
+
+    graph = old_graph or {}  # type: Graph
+
     # The deque is used to implement breadth-first traversal.
     # TODO: Consider whether to go depth-first instead.  This may
     # affect the order in which we process files within import cycles.

mypy/checker.py

@@ -211,6 +211,24 @@ def __init__(self, errors: Errors, modules: Dict[str, MypyFile], options: Option
         # for processing module top levels in fine-grained incremental mode.
         self.recurse_into_functions = True
 
+    def reset(self) -> None:
+        """Cleanup stale state that might be left over from a typechecking run.
+
+        This allows us to reuse TypeChecker objects in fine-grained
+        incremental mode.
+        """
+        # TODO: verify this is still actually worth it over creating new checkers
+        self.partial_reported.clear()
+        self.module_refs.clear()
+        self.binder = ConditionalTypeBinder()
+        self.type_map.clear()
+
+        assert self.inferred_attribute_types is None
+        assert self.partial_types == []
+        assert self.deferred_nodes == []
+        assert len(self.scope.stack) == 1
+        assert self.partial_types == []
+
     def check_first_pass(self) -> None:
         """Type check the entire file, but defer functions with unresolved references.
 

mypy/dmypy_server.py

@@ -282,10 +282,12 @@ def initialize_fine_grained(self, sources: List[mypy.build.BuildSource]) -> Dict
         if self.options.use_fine_grained_cache:
             # Pull times and hashes out of the saved_cache and stick them into
             # the fswatcher, so we pick up the changes.
-            for meta, mypyfile, type_map in manager.saved_cache.values():
-                if meta.mtime is None: continue
+            for state in self.fine_grained_manager.graph.values():
+                meta = state.meta
+                if meta is None: continue
+                assert state.path is not None
                 self.fswatcher.set_file_data(
-                    mypyfile.path,
+                    state.path,
                     FileData(st_mtime=float(meta.mtime), st_size=meta.size, md5=meta.hash))
 
             # Run an update