debugged test_helpers_file

pydra/design/shell.py

@@ -669,7 +669,7 @@ def remaining_positions(
         If multiple fields have the same position
     """
     if num_args is None:
-        num_args = len(args)
+        num_args = len(args) - 1  # Subtract 1 for the 'additional_args' field
     # Check for multiple positions
     positions = defaultdict(list)
     for arg in args:

pydra/engine/helpers_file.py

@@ -119,10 +119,9 @@ def template_update(
         for field in list_fields(definition)
         if isinstance(field, shell.outarg)
         and field.path_template
-        and getattr(definition, field.name) is not False
+        and getattr(definition, field.name)
         and all(
-            getattr(definition, required_field) is not None
-            for required_field in field.requires
+            getattr(definition, required_field) for required_field in field.requires
         )
     ]
 
@@ -164,7 +163,7 @@ def template_update_single(
             raise TypeError(
                 f"type of '{field.name}' is Path, consider using Union[Path, bool]"
             )
-        if inp_val_set is not attr.NOTHING and not is_lazy(inp_val_set):
+        if inp_val_set is not None and not is_lazy(inp_val_set):
             inp_val_set = TypeParser(ty.Union[OUTPUT_TEMPLATE_TYPES])(inp_val_set)
     elif spec_type == "output":
         if not TypeParser.contains_type(FileSet, field.type):
@@ -252,6 +251,8 @@ def _string_template_formatting(field, template, definition, input_values):
         if fld_name not in input_values:
             raise AttributeError(f"{fld_name} is not provided in the input")
         fld_value = input_values[fld_name]
+        if isinstance(fld_value, Path):  # Remove path
+            fld_value = fld_value.name
         if fld_value is attr.NOTHING:
             # if value is NOTHING, nothing should be added to the command
             return attr.NOTHING

pydra/engine/specs.py

@@ -945,27 +945,14 @@ def _command_args(
                 pos_args.append(self._command_shelltask_executable(field, value))
             elif name == "additional_args":
                 continue
-            elif name == "args":
-                pos_val = self._command_shelltask_args(field, value)
-                if pos_val:
-                    pos_args.append(pos_val)
             else:
-                if name in modified_inputs:
-                    pos_val = self._command_pos_args(
-                        field=field,
-                        value=value,
-                        inputs=inputs,
-                        root=root,
-                        output_dir=output_dir,
-                    )
-                else:
-                    pos_val = self._command_pos_args(
-                        field=field,
-                        value=value,
-                        output_dir=output_dir,
-                        inputs=inputs,
-                        root=root,
-                    )
+                pos_val = self._command_pos_args(
+                    field=field,
+                    value=value,
+                    inputs=inputs,
+                    root=root,
+                    output_dir=output_dir,
+                )
                 if pos_val:
                     pos_args.append(pos_val)
 
@@ -1024,10 +1011,6 @@ def _command_pos_args(
 
             self._positions_provided.append(field.position)
 
-            # Shift non-negatives up to allow executable to be 0
-            # Shift negatives down to allow args to be -1
-            field.position += 1 if field.position >= 0 else -1
-
         if value and isinstance(value, str):
             if root:  # values from templates
                 value = value.replace(str(output_dir), f"{root}{output_dir}")

pydra/engine/tests/test_helpers_file.py

@@ -1,12 +1,14 @@
 import typing as ty
 import sys
+import os
 from pathlib import Path
 from unittest.mock import Mock
 import pytest
 from fileformats.generic import File
 from pydra.engine.specs import ShellDef, ShellOutputs
 from pydra.design import shell
-from ..helpers_file import (
+from pydra.engine.helpers import list_fields
+from pydra.engine.helpers_file import (
     ensure_list,
     MountIndentifier,
     copy_nested_files,
@@ -376,18 +378,21 @@ class Outputs(ShellOutputs):
     defn = MyCommand(in_file=filename)
     assert defn.cmdline == f"my {filename}"
     defn.optional = True
-    assert defn.cmdline == f"my {filename} --opt 'file.out'"
+    file_out_path = os.path.join(os.getcwd(), "file.out")
+    if " " in file_out_path:
+        file_out_path = f"'{file_out_path}'"
+    assert defn.cmdline == f"my {filename} --opt {file_out_path}"
     defn.optional = False
     assert defn.cmdline == f"my {filename}"
     defn.optional = "custom-file-out.txt"
     assert defn.cmdline == f"my {filename} --opt custom-file-out.txt"
 
 
-def test_template_formatting(tmp_path):
+def test_template_formatting(tmp_path: Path):
     field = Mock()
     field.name = "grad"
     field.argstr = "--grad"
-    field.metadata = {"output_file_template": ("{in_file}.bvec", "{in_file}.bval")}
+    field.path_template = ("{in_file}.bvec", "{in_file}.bval")
     inputs = Mock()
     inputs_dict = {"in_file": "/a/b/c/file.txt", "grad": True}