update linter

WDL/Lint.py

@@ -520,8 +520,10 @@ def decl(self, obj: Tree.Decl) -> Any:
     def call(self, obj: Tree.Call) -> Any:
         for name, inp_expr in obj.inputs.items():
             decl = _find_input_decl(obj, name)
-            if not inp_expr.type.coerces(decl.type, check_quant=True) and not _is_array_coercion(
-                decl.type, inp_expr.type
+            # implicitly consider optional, the type of an input with a default
+            decltype = decl.type.copy(optional=True) if decl.expr else decl.type
+            if not inp_expr.type.coerces(decltype, check_quant=True) and not _is_array_coercion(
+                decltype, inp_expr.type
             ):
                 msg = "input {} {} = :{}:".format(str(decl.type), decl.name, str(inp_expr.type))
                 self.add(obj, msg, inp_expr.pos)

WDL/Tree.py

@@ -613,13 +613,13 @@ def typecheck_input(
             for name, expr in self.inputs.items():
                 try:
                     decl = self.callee.available_inputs[name]
+                    # implicitly consider optional, the type of an input with a default
+                    decltype = decl.type.copy(optional=True) if decl.expr else decl.type
                     errors.try1(
                         lambda expr=expr, decl=decl: expr.infer_type(
                             type_env, stdlib, check_quant=check_quant, struct_types=struct_types
-                        ).typecheck(decl.type.copy(optional=True) if decl.expr else decl.type)
+                        ).typecheck(decltype)
                     )
-                    # If the input includes a default, then we implicitly made None acceptable even
-                    # if the declared type wasn't optional.
                 except KeyError:
                     errors.append(Error.NoSuchInput(expr, name))
                 if name in required_inputs:

WDL/runtime/workflow.py

@@ -415,8 +415,10 @@ def __getstate__(self) -> Dict[str, Any]:
 def _coerce_call_inputs(
     input_values: Env.Bindings[Value.Base], input_decls: Env.Bindings[Tree.Decl]
 ) -> Env.Bindings[Value.Base]:
-    # fixup pass: if explicit None value is supplied for an input that has a default value AND a
-    # non-optional type, make it as if the value were absent (so that the default will be used)
+    # Fixup pass: if None value is supplied for an input that has a default expression AND
+    # non-optional type, remove the value entirely so that the default will be used.
+    # In contrast, if the input declaration has an -explicitly- optional type, then we do pass None
+    # to override the default, if any.
     input_values = input_values.filter(
         lambda b: not (
             isinstance(b.value, Value.Null)

tests/test_3corpi.py

@@ -460,7 +460,7 @@ class BioWDLTasks(unittest.TestCase):
 @wdl_corpus(
     ["test_corpi/biowdl/aligning/**"],
     expected_lint={
-        "OptionalCoercion": 12,
+        "OptionalCoercion": 11,
         "UnusedDeclaration": 12,
         "NonemptyCoercion": 1,
         "NameCollision": 1,
@@ -507,7 +507,6 @@ class BioWDLSomaticVariantCalling(unittest.TestCase):
     expected_lint={
         "UnusedDeclaration": 8,
         "SelectArray": 2,
-        "OptionalCoercion": 2,
         "NonemptyCoercion": 3,
         "UnusedCall": 1,
         "UnverifiedStruct": 1,

tests/test_7runner.py

@@ -956,3 +956,5 @@ def test_implicitly_optional_input_with_default(self):
         self.assertEqual(outp["results"], ["AliceCarol", None])
         outp = self._run(caller, {"b": "Bas"})
         self.assertEqual(outp["results"], ["AliceBas", "Bas"])
+        outp = self._run(caller, {"a": "Alyssa"})
+        self.assertEqual(outp["results"], ["Alyssa", None])