v1.0 conformance tests inspired fixes

Author: mr-c

cwltool/argparser.py

@@ -638,8 +638,7 @@ def arg_parser() -> argparse.ArgumentParser:
     return parser
 
 
-def get_default_args():
-    # type: () -> Dict[str, Any]
+def get_default_args() -> Dict[str, Any]:
     """Get default values of cwltool's command line options."""
     ap = arg_parser()
     args = ap.parse_args([])
@@ -649,20 +648,21 @@ def get_default_args():
 class FSAction(argparse.Action):
     objclass = None  # type: str
 
-    def __init__(self, option_strings, dest, nargs=None, **kwargs):
-        # type: (List[str], str, Any, **Any) -> None
+    def __init__(
+        self, option_strings: List[str], dest: str, nargs: Any = None, **kwargs: Any
+    ) -> None:
         """Fail if nargs is used."""
         if nargs is not None:
             raise ValueError("nargs not allowed")
         super(FSAction, self).__init__(option_strings, dest, **kwargs)
 
     def __call__(
         self,
-        parser,  # type: argparse.ArgumentParser
-        namespace,  # type: argparse.Namespace
-        values,  # type: Union[AnyStr, Sequence[Any], None]
-        option_string=None,  # type: Optional[str]
-    ):  # type: (...) -> None
+        parser: argparse.ArgumentParser,
+        namespace: argparse.Namespace,
+        values: Union[AnyStr, Sequence[Any], None],
+        option_string: Optional[str] = None,
+    ) -> None:
         setattr(
             namespace,
             self.dest,
@@ -676,20 +676,21 @@ def __call__(
 class FSAppendAction(argparse.Action):
     objclass = None  # type: str
 
-    def __init__(self, option_strings, dest, nargs=None, **kwargs):
-        # type: (List[str], str, Any, **Any) -> None
+    def __init__(
+        self, option_strings: List[str], dest: str, nargs: Any = None, **kwargs: Any
+    ) -> None:
         """Initialize."""
         if nargs is not None:
             raise ValueError("nargs not allowed")
         super(FSAppendAction, self).__init__(option_strings, dest, **kwargs)
 
     def __call__(
         self,
-        parser,  # type: argparse.ArgumentParser
-        namespace,  # type: argparse.Namespace
-        values,  # type: Union[AnyStr, Sequence[Any], None]
-        option_string=None,  # type: Optional[str]
-    ):  # type: (...) -> None
+        parser: argparse.ArgumentParser,
+        namespace: argparse.Namespace,
+        values: Union[AnyStr, Sequence[Any], None],
+        option_string: Optional[str] = None,
+    ) -> None:
         g = getattr(namespace, self.dest)
         if not g:
             g = []
@@ -719,15 +720,14 @@ class DirectoryAppendAction(FSAppendAction):
 
 
 def add_argument(
-    toolparser,
-    name,
-    inptype,
-    records,
-    description="",
-    default=None,
-    input_required=True,
-):
-    # type: (argparse.ArgumentParser, str, Any, List[str], str, Any, bool) -> None
+    toolparser: argparse.ArgumentParser,
+    name: str,
+    inptype: Any,
+    records: List[str],
+    description: str = "",
+    default: Any = None,
+    input_required: bool = True,
+) -> None:
     if len(name) == 1:
         flag = "-"
     else:

cwltool/builder.py

@@ -230,8 +230,8 @@ def bind_input(
         if lead_pos is None:
             lead_pos = []
 
-        bindings = []  # type: List[MutableMapping[str, str]]
-        binding = {}  # type: Union[MutableMapping[str, str], CommentedMap]
+        bindings = []  # type: List[MutableMapping[str, Union[str, List[int]]]]
+        binding = {}  # type: Union[MutableMapping[str, Union[str, List[int]]], CommentedMap]
         value_from_expression = False
         if "inputBinding" in schema and isinstance(
             schema["inputBinding"], MutableMapping
@@ -484,7 +484,7 @@ def addsf(
         # Position to front of the sort key
         if binding:
             for bi in bindings:
-                bi["position"] = binding["position"] + bi["position"]
+                bi["position"] = cast(List[int], binding["position"]) + cast(List[int], bi["position"])
             bindings.append(binding)
 
         return bindings

cwltool/process.py

@@ -916,8 +916,7 @@ def inc(d):  # type: (List[int]) -> None
             builder.resources = self.evalResources(builder, runtime_context)
         return builder
 
-    def evalResources(self, builder, runtimeContext):
-        # type: (Builder, RuntimeContext) -> Dict[str, int]
+    def evalResources(self, builder: Builder, runtimeContext: RuntimeContext) -> Dict[str, int]:
         resourceReq, _ = self.get_requirement("ResourceRequirement")
         if resourceReq is None:
             resourceReq = {}
@@ -939,19 +938,18 @@ def evalResources(self, builder, runtimeContext):
             "outdirMax": 1024,
         }  # type: Dict[str, int]
         for a in ("cores", "ram", "tmpdir", "outdir"):
-            mn = None  # type: Optional[Union[str, int]]
-            mx = None  # type: Optional[Union[str, int]]
+            mn = mx = None  # type: Optional[int]
             if resourceReq.get(a + "Min"):
-                mn = eval_resource(builder, cast(int, resourceReq[a + "Min"]))
+                mn = cast(int, eval_resource(builder, cast(Union[str, int], resourceReq[a + "Min"])))
             if resourceReq.get(a + "Max"):
-                mx = eval_resource(builder, cast(int, resourceReq[a + "Max"]))
+                mx = cast(int, eval_resource(builder, cast(Union[str, int], resourceReq[a + "Max"])))
             if mn is None:
                 mn = mx
             elif mx is None:
                 mx = mn
 
             if mn is not None:
-                request[a + "Min"] = cast(int, mn)
+                request[a + "Min"] = mn
                 request[a + "Max"] = cast(int, mx)
 
         if runtimeContext.select_resources is not None:

setup.py

@@ -97,7 +97,7 @@
         "ruamel.yaml >= 0.12.4, <= 0.16.5",
         "rdflib >= 4.2.2, < 4.3.0",
         "shellescape >= 3.4.1, < 3.5",
-        "schema-salad >= 5.0.20200126033820, < 6",
+        "schema-salad >= 5.1, < 6",
         "mypy-extensions",
         "psutil",
         "prov == 1.5.1",