wip

WDL/Error.py

@@ -69,9 +69,6 @@ def __init__(self, pos: SourcePosition, import_uri: str, message: Optional[str]
         self.pos = pos
 
 
-TVSourceNode = TypeVar("TVSourceNode", bound="SourceNode")
-
-
 @total_ordering
 class SourceNode:
     """Base class for an AST node, recording the source position"""
@@ -83,7 +80,7 @@ class SourceNode:
     Source position for this AST node
     """
 
-    parent: Optional[TVSourceNode] = None
+    parent: Optional["SourceNode"] = None
     """
     :type: Optional[SourceNode]
 
@@ -93,7 +90,7 @@ class SourceNode:
     def __init__(self, pos: SourcePosition) -> None:
         self.pos = pos
 
-    def __lt__(self, rhs: TVSourceNode) -> bool:
+    def __lt__(self, rhs: "SourceNode") -> bool:
         if isinstance(rhs, SourceNode):
             return (
                 self.pos.abspath,
@@ -110,12 +107,12 @@ def __lt__(self, rhs: TVSourceNode) -> bool:
             )
         return False
 
-    def __eq__(self, rhs: TVSourceNode) -> bool:
+    def __eq__(self, rhs: "SourceNode") -> bool:
         assert isinstance(rhs, SourceNode)
         return self.pos == rhs.pos
 
     @property
-    def children(self: TVSourceNode) -> Iterable[TVSourceNode]:
+    def children(self) -> Iterable["SourceNode"]:
         """
         :type: Iterable[SourceNode]
 

WDL/__init__.py

@@ -287,7 +287,9 @@ def values_from_json(
     return ans
 
 
-def values_to_json(values_env: Env.Bindings[Union[Value.Base, Tree.Decl, Type.Base]], namespace: str = "") -> Dict[str, Any]:
+def values_to_json(
+    values_env: Env.Bindings[Union[Value.Base, Tree.Decl, Type.Base]], namespace: str = ""
+) -> Dict[str, Any]:
     """
     Convert a ``WDL.Env.Bindings[WDL.Value.Base]`` to a dict which ``json.dumps`` to
     Cromwell-style JSON.

WDL/runtime/workflow.py

@@ -172,7 +172,7 @@ def __init__(
 
         from .. import values_to_json
 
-        self.values_to_json = values_to_json  # pyre-ignore
+        self.values_to_json = values_to_json  # type: ignore
 
         # Preprocess inputs: if None value is supplied for an input declared with a default but
         # without the ? type quantifier, remove the binding entirely so that the default will be
@@ -264,7 +264,7 @@ def step(
         doing so after initialization and after each ``call_finished()`` invocation, until at last
         the workflow outputs are available.
         """
-        runnable = []
+        runnable: List[str] = []
         while True:
             # select a job whose dependencies are all finished
             if not runnable:
@@ -346,7 +346,7 @@ def _do_job(
 
         # for all non-Gather nodes, derive the environment by merging the outputs of all the
         # dependencies (+ any current scatter variable bindings)
-        scatter_vars = Env.Bindings()
+        scatter_vars: Env.Bindings[Value.Base] = Env.Bindings()
         for p in job.scatter_stack:
             scatter_vars = Env.Bindings(p[1], scatter_vars)
         # pyre-ignore
@@ -396,11 +396,12 @@ def _do_job(
 
         if isinstance(job.node, Tree.Call):
             # evaluate input expressions
-            call_inputs = Env.Bindings()
+            call_name = job.node.name
+            call_inputs: Env.Bindings[Value.Base] = Env.Bindings()
             for name, expr in job.node.inputs.items():
                 call_inputs = call_inputs.bind(name, expr.eval(env, stdlib=stdlib))
             # check workflow inputs for additional inputs supplied to this call
-            for b in self.inputs.enter_namespace(job.node.name):
+            for b in self.inputs.enter_namespace(call_name):
                 call_inputs = call_inputs.bind(b.name, b.value)
 
             # coerce inputs to required types (treating inputs with defaults as optional even if
@@ -426,7 +427,7 @@ def _do_job(
             call_inputs = Value.rewrite_env_paths(
                 call_inputs,
                 lambda v: _check_path_allowed(
-                    cfg, self.fspath_allowlist, f"call {job.node.name} input", v
+                    cfg, self.fspath_allowlist, f"call {call_name} input", v
                 ),
             )
             # issue CallInstructions
@@ -470,7 +471,7 @@ def _scatter(
 ) -> Iterable[_Job]:
     # we'll be tracking, for each body node ID, the IDs of the potentially multiple corresponding
     # jobs scheduled
-    multiplex = {}
+    multiplex: Dict[str, Set[str]] = {}
     for body_node in section.body:
         multiplex[body_node.workflow_node_id] = set()
         if isinstance(body_node, Tree.WorkflowSection):
@@ -479,10 +480,11 @@ def _scatter(
 
     # evaluate scatter array or boolean condition
     v = section.expr.eval(env, stdlib=stdlib)
-    array = []
+    array: List[Optional[Value.Base]] = []
     if isinstance(section, Tree.Scatter):
         assert isinstance(v, Value.Array)
-        array = v.value
+        for v_i in v.value:
+            array.append(v_i)
     else:
         assert isinstance(v, Value.Boolean)
         if v.value:
@@ -653,7 +655,7 @@ def _gather(
         assert False
 
     # for each such name,
-    ans = Env.Bindings()
+    ans: Env.Bindings[Value.Base] = Env.Bindings()
     ns = [leaf.name] if isinstance(leaf, Tree.Call) else []
     for name in names:
         # gather the corresponding values
@@ -662,7 +664,7 @@ def _gather(
         assert v0 is None or isinstance(v0, Value.Base)
         # bind the array, singleton value, or None as appropriate
         if isinstance(gather.section, Tree.Scatter):
-            rhs = Value.Array((v0.type if v0 else Type.Any()), values)
+            rhs: Value.Base = Value.Array((v0.type if v0 else Type.Any()), values)
         else:
             assert isinstance(gather.section, Tree.Conditional)
             assert len(values) <= 1
@@ -707,17 +709,19 @@ def _virtualize_filename(self, filename: str) -> str:
         with open(filename, "rb") as f:
             for chunk in iter(lambda: f.read(1048576), b""):
                 hasher.update(chunk)
-        cache_in = Env.Bindings().bind("file_sha256", Value.String(hasher.hexdigest()))
+        cache_in: Env.Bindings[Value.Base] = Env.Bindings()
+        cache_in = cache_in.bind("file_sha256", Value.String(hasher.hexdigest()))
         cache_key = "write_/" + Value.digest_env(cache_in)
-        cache_out_types = Env.Bindings().bind("file", Type.File())
+        cache_out_types: Env.Bindings[Type.Base] = Env.Bindings()
+        cache_out_types = cache_out_types.bind("file", Type.File())
         cache_out = self.cache.get(cache_key, cache_in, cache_out_types)
         if cache_out:
             filename = cache_out.resolve("file").value
         else:
             # otherwise, put our newly-written file to the cache, and proceed to use it
             self.cache.put(
                 cache_key,
-                Env.Bindings().bind("file", Value.File(filename)),
+                Env.Bindings(Env.Binding("file", Value.File(filename))),
                 run_dir=self.state.run_dir,
             )
 
@@ -873,7 +877,7 @@ def run_local_workflow(
         cache = _cache
         if not cache:
             cache = cleanup.enter_context(new_call_cache(cfg, logger))
-            assert _thread_pools is None
+            assert cache and _thread_pools is None
         if not _thread_pools:
             cache.flock(logfile, exclusive=True)  # flock top-level workflow.log
         write_values_json(inputs, os.path.join(run_dir, "inputs.json"), namespace=workflow.name)
@@ -975,7 +979,7 @@ def _workflow_main_loop(
         with compose_coroutines(
             [
                 (
-                    lambda kwargs, cor=cor: cor(
+                    lambda kwargs, cor=cor: cor(  # type: ignore
                         cfg, logger, run_id_stack, run_dir, workflow, **kwargs
                     )
                 )
@@ -1071,7 +1075,7 @@ def _workflow_main_loop(
     except Exception as exn:
         tbtxt = traceback.format_exc()
         logger.debug(tbtxt)
-        cause = exn
+        cause: BaseException = exn
         while isinstance(cause, RunFailed) and cause.__cause__:
             cause = cause.__cause__
         wrapper = RunFailed(workflow, run_id_stack[-1], run_dir)

stubs/logging/__init__.py

@@ -4,3 +4,6 @@
 class Logger(OriginalLogger):
     def notice(self, *args, **kwargs) -> None: ...
     def verbose(self, *args, **kwargs) -> None: ...
+
+def getLogger(name: str) -> Logger:
+    ...