Merge remote-tracking branch 'upstream/issues/5004-wdl-virtualize-onl…

…y-at-task-boundaries' into issues/5004-wdl-virtualize-only-at-task-boundaries

src/toil/wdl/wdltoil.py

@@ -535,36 +535,26 @@ def log_bindings(log_function: Callable[..., None], message: str, all_bindings:
         elif isinstance(bindings, Promise):
             log_function("<Unfulfilled promise for bindings>")
 
-def get_supertype(types: Sequence[Optional[WDL.Type.Base]]) -> WDL.Type.Base:
+def get_supertype(types: Sequence[WDL.Type.Base]) -> WDL.Type.Base:
     """
     Get the supertype that can hold values of all the given types.
     """
-
-    if None in types:
-        # Need to allow optional values
-        if len(types) == 1:
-            # Only None is here
-            return WDL.Type.Any(optional=True)
-        if len(types) == 2:
-            # None and something else
-            for item in types:
-                if item is not None:
-                    # Return the type that's actually there, but make optional if not already.
-                    return item.copy(optional=True)
-            raise RuntimeError("Expected non-None in types could not be found")
-        else:
-            # Multiple types, and some nulls, so we need an optional Any.
-            return WDL.Type.Any(optional=True)
-    else:
-        if len(types) == 1:
-            # Only one type. It isn't None.
-            the_type = types[0]
-            if the_type is None:
-                raise RuntimeError("The supertype cannot be None.")
-            return the_type
+    supertype = None
+    optional = False
+    for typ in types:
+        if isinstance(typ, WDL.Type.Any):
+            # ignore an Any type, as we represent a bottom type as Any. See https://miniwdl.readthedocs.io/en/latest/WDL.html#WDL.Type.Any
+            # and https://github.com/openwdl/wdl/blob/e43e042104b728df1f1ad6e6145945d2b32331a6/SPEC.md?plain=1#L1484
+            optional = optional or typ.optional
+        elif supertype is None:
+            supertype = typ
+            optional = optional or typ.optional
         else:
-            # Multiple types (or none). Assume Any
-            return WDL.Type.Any()
+            # We have conflicting types
+            raise RuntimeError(f"Cannot generate a supertype from conflicting types: {types}")
+    if supertype is None:
+        return WDL.Type.Any(null=optional)  # optional flag isn't used in Any
+    return supertype.copy(optional=optional)
 
 
 def for_each_node(root: WDL.Tree.WorkflowNode) -> Iterator[WDL.Tree.WorkflowNode]:
@@ -3406,7 +3396,7 @@ def run(self, file_store: AbstractFileStore) -> WDLBindings:
             # Problem: the WDL type types are not hashable, so we need to do bad N^2 deduplication
             observed_types = []
             for env in new_bindings:
-                binding_type = env.resolve(name).type if env.has_binding(name) else None
+                binding_type = env.resolve(name).type if env.has_binding(name) else WDL.Type.Any()
                 if binding_type not in observed_types:
                     observed_types.append(binding_type)
             # Get the supertype of those types