wip

WDL/CLI.py

@@ -145,7 +145,7 @@ def __call__(self, parser, namespace, values, option_string=None):
         # importlib_metadata doesn't seem to provide EntryPoint.dist to get from an entry point to
         # the metadata of the package providing it; continuing to use pkg_resources for this. Risk
         # that they give inconsistent results?
-        import pkg_resources
+        import pkg_resources  # type: ignore
 
         for group in runtime.config.default_plugins().keys():
             group = f"miniwdl.plugin.{group}"
@@ -1116,7 +1116,8 @@ def runner_input_json_file(available_inputs, namespace, input_file, downloadable
     if input_file:
         input_file = input_file.strip()
     if input_file:
-        import yaml  # delayed heavy import
+        # delayed heavy import:
+        import yaml  # type: ignore
 
         input_json = None
         if input_file[0] == "{":
@@ -1745,7 +1746,7 @@ def configure(cfg=None, show=False, force=False, **kwargs):
         die("`miniwdl configure` is for interactive use")
 
     from datetime import datetime
-    import bullet
+    import bullet  # type: ignore
     from xdg import XDG_CONFIG_HOME
 
     miniwdl_version = pkg_version()
@@ -2148,6 +2149,7 @@ def _type_to_input_template(ty: Type.Base):
     """
     if isinstance(ty, Type.StructInstance):
         ans = {}
+        assert ty.members
         for member_name, member_type in ty.members.items():
             if not member_type.optional:  # TODO: opt in to these
                 ans[member_name] = _type_to_input_template(member_type)

WDL/runtime/__init__.py

@@ -61,4 +61,4 @@ def run(
     if "max_tasks" in run_kwargs and isinstance(exe, Tree.Task):
         del run_kwargs["max_tasks"]  # N/A to run_local_task
     entrypoint = run_local_task if isinstance(exe, Tree.Task) else run_local_workflow
-    return entrypoint(cfg, exe, inputs, **run_kwargs)  # pyre-ignore
+    return entrypoint(cfg, exe, inputs, **run_kwargs)  # type: ignore

WDL/runtime/backend/cli_subprocess.py

@@ -118,8 +118,8 @@ def _run(self, logger: logging.Logger, terminating: Callable[[], bool], command:
                 poll_cli_log()
             if terminating():
                 raise Terminated()
-            assert isinstance(exit_code, int)
-            return exit_code
+        assert isinstance(exit_code, int)
+        return exit_code
 
     @abstractproperty
     def cli_name(self) -> str:

WDL/runtime/workflow.py

@@ -1142,15 +1142,15 @@ def scan_uri(v: Union[Value.File, Value.Directory]) -> str:
     Value.rewrite_env_paths(inputs, scan_uri)
     if not uris:
         return
-    logger.notice(_("downloading input URIs", count=len(uris)))  # pyre-fixme
+    logger.notice(_("downloading input URIs", count=len(uris)))
 
     # download them on the thread pool (but possibly further limiting concurrency)
     download_concurrency = cfg.get_int("scheduler", "download_concurrency")
     if download_concurrency <= 0:
         download_concurrency = 999999
-    ops = {}
+    ops: Dict[futures.Future[Tuple[bool, str]], str] = {}
     incomplete = len(uris)
-    outstanding = set()
+    outstanding: Set[futures.Future[Tuple[bool, str]]] = set()
     downloaded_bytes = 0
     cached_hits = 0
     exn = None
@@ -1208,7 +1208,7 @@ def scan_uri(v: Union[Value.File, Value.Directory]) -> str:
 
     if exn:
         raise exn
-    logger.notice(  # pyre-fixme
+    logger.notice(
         _(
             "processed input URIs",
             cached=cached_hits,

stubs/logging/__init__.py

@@ -0,0 +1,6 @@
+from logging import Logger as OriginalLogger
+from logging import DEBUG, INFO, WARNING, ERROR, CRITICAL
+
+class Logger(OriginalLogger):
+    def notice(self, *args, **kwargs) -> None: ...
+    def verbose(self, *args, **kwargs) -> None: ...