fixing up errors in test_shell

Author: tclose

pydra/design/shell.py

@@ -22,7 +22,12 @@
     make_task_def,
     NO_DEFAULT,
 )
-from pydra.utils.typing import is_fileset_or_union, MultiInputObj
+from pydra.utils.typing import (
+    is_fileset_or_union,
+    MultiInputObj,
+    is_optional,
+    optional_type,
+)
 
 if ty.TYPE_CHECKING:
     from pydra.engine.specs import ShellDef
@@ -94,11 +99,15 @@ class arg(Arg):
 
     argstr: str | None = ""
     position: int | None = None
-    sep: str | None = attrs.field(default=None)
+    sep: str | None = attrs.field()
     allowed_values: list | None = None
     container_path: bool = False  # IS THIS STILL USED??
     formatter: ty.Callable | None = None
 
+    @sep.default
+    def _sep_default(self):
+        return " " if self.type is tuple or ty.get_origin(self.type) is tuple else None
+
     @sep.validator
     def _validate_sep(self, _, sep):
         if self.type is ty.Any:
@@ -107,7 +116,10 @@ def _validate_sep(self, _, sep):
             tp = ty.get_args(self.type)[0]
         else:
             tp = self.type
+        if is_optional(tp):
+            tp = optional_type(tp)
         origin = ty.get_origin(tp) or tp
+
         if (
             inspect.isclass(origin)
             and issubclass(origin, ty.Sequence)

pydra/design/tests/test_shell.py

@@ -162,7 +162,7 @@ def test_interface_template_more_complex():
 
     Cp = shell.define(
         (
-            "cp <in_fs_objects:fs-object,...> <out|out_dir:directory> "
+            "cp <in_fs_objects:fs-object+> <out|out_dir:directory> "
             "-R<recursive> "
             "--text-arg <text_arg?> "
             "--int-arg <int_arg:int?> "
@@ -187,7 +187,9 @@ def test_interface_template_more_complex():
             help=shell.EXECUTABLE_HELP_STRING,
         ),
         shell.arg(
-            name="in_fs_objects", type=MultiInputObj[FsObject], position=1, sep=" "
+            name="in_fs_objects",
+            type=MultiInputObj[FsObject],
+            position=1,
         ),
         output,
         shell.arg(name="recursive", argstr="-R", type=bool, default=False, position=3),
@@ -210,6 +212,7 @@ def test_interface_template_more_complex():
             argstr="--tuple-arg",
             type=tuple[int, str] | None,
             default=None,
+            sep=" ",
             position=6,
         ),
         ShellDef.additional_args,
@@ -245,7 +248,7 @@ def test_interface_template_with_overrides_and_optionals():
 
     Cp = shell.define(
         (
-            "cp <in_fs_objects:fs-object,...> <out|out_dir:directory> <out|out_file:file?> "
+            "cp <in_fs_objects:fs-object+> <out|out_dir:directory> <out|out_file:file?> "
             "-R<recursive> "
             "--text-arg <text_arg> "
             "--int-arg <int_arg:int?> "
@@ -284,7 +287,9 @@ def test_interface_template_with_overrides_and_optionals():
             help=shell.EXECUTABLE_HELP_STRING,
         ),
         shell.arg(
-            name="in_fs_objects", type=MultiInputObj[FsObject], position=1, sep=" "
+            name="in_fs_objects",
+            type=MultiInputObj[FsObject],
+            position=1,
         ),
         shell.arg(
             name="recursive",
@@ -306,6 +311,7 @@ def test_interface_template_with_overrides_and_optionals():
             name="tuple_arg",
             argstr="--tuple-arg",
             type=tuple[int, str],
+            sep=" ",
             position=5,
         ),
     ] + outargs + [ShellDef.additional_args]
@@ -332,7 +338,7 @@ def test_interface_template_with_defaults():
 
     Cp = shell.define(
         (
-            "cp <in_fs_objects:fs-object,...> <out|out_dir:directory> "
+            "cp <in_fs_objects:fs-object+> <out|out_dir:directory> "
             "-R<recursive=True> "
             "--text-arg <text_arg='foo'> "
             "--int-arg <int_arg:int=99> "
@@ -357,7 +363,9 @@ def test_interface_template_with_defaults():
             help=shell.EXECUTABLE_HELP_STRING,
         ),
         shell.arg(
-            name="in_fs_objects", type=MultiInputObj[FsObject], position=1, sep=" "
+            name="in_fs_objects",
+            type=MultiInputObj[FsObject],
+            position=1,
         ),
         output,
         shell.arg(name="recursive", argstr="-R", type=bool, default=True, position=3),
@@ -400,7 +408,7 @@ def test_interface_template_with_type_overrides():
 
     Cp = shell.define(
         (
-            "cp <in_fs_objects:fs-object,...> <out|out_dir:directory> "
+            "cp <in_fs_objects:fs-object+> <out|out_dir:directory> "
             "-R<recursive> "
             "--text-arg <text_arg> "
             "--int-arg <int_arg> "
@@ -426,7 +434,9 @@ def test_interface_template_with_type_overrides():
             help=shell.EXECUTABLE_HELP_STRING,
         ),
         shell.arg(
-            name="in_fs_objects", type=MultiInputObj[FsObject], position=1, sep=" "
+            name="in_fs_objects",
+            type=MultiInputObj[FsObject],
+            position=1,
         ),
         output,
         shell.arg(name="recursive", argstr="-R", type=bool, default=False, position=3),

pydra/engine/specs.py

@@ -18,7 +18,7 @@
 import cloudpickle as cp
 from fileformats.generic import FileSet
 from pydra.utils.messenger import AuditFlag, Messenger
-from pydra.utils.typing import TypeParser, is_optional, non_optional_type
+from pydra.utils.typing import TypeParser, is_optional, optional_type
 from .helpers import (
     attrs_fields,
     attrs_values,
@@ -1130,7 +1130,7 @@ def _command_pos_args(
         cmd_add = []
         # formatter that creates a custom command argument
         # it can take the value of the field, all inputs, or the value of other fields.
-        tp = non_optional_type(field.type) if is_optional(field.type) else field.type
+        tp = optional_type(field.type) if is_optional(field.type) else field.type
         if field.formatter:
             call_args = inspect.getfullargspec(field.formatter)
             call_args_val = {}

pydra/utils/typing.py

@@ -1037,22 +1037,24 @@ def label_str(self):
 
 
 def is_union(type_: type) -> bool:
+    """Checks whether a type is a Union, in either ty.Union[T, U] or T | U form"""
     return ty.get_origin(type_) in UNION_TYPES
 
 
 def is_optional(type_: type) -> bool:
-    """Check if the type is Optional"""
+    """Check if the type is Optional, i.e. a union containing None"""
     if is_union(type_):
         return any(a is type(None) or is_optional(a) for a in ty.get_args(type_))
     return False
 
 
-def non_optional_type(type_: type) -> type:
+def optional_type(type_: type) -> type:
+    """Gets the non-None args of an optional type (i.e. a union with a None arg)"""
     if is_optional(type_):
-        non_optional = [a for a in ty.get_args(type_) if a is not type(None)]
-        if len(non_optional) == 1:
-            return non_optional[0]
-        return ty.Union[tuple(non_optional)]
+        non_none = [a for a in ty.get_args(type_) if a is not type(None)]
+        if len(non_none) == 1:
+            return non_none[0]
+        return ty.Union[tuple(non_none)]
     return type_