changing template formatting when value (or default) is False

pydra/engine/helpers.py

@@ -24,6 +24,7 @@
     File,
     Directory,
     attr_fields,
+    attr_field,
     Result,
     LazyField,
     MultiOutputObj,
@@ -884,6 +885,12 @@ def argstr_formatting(argstr, inputs, value_updates=None):
         if fld_value is attr.NOTHING:
             # if value is NOTHING, nothing should be added to the command
             val_dict[fld_name] = ""
+        # if value is False, but the field has a template the output field should not be created
+        elif (
+            fld_value is False
+            and "output_file_template" in attr_field(inputs, fld_name).metadata
+        ):
+            val_dict[fld_name] = ""
         else:
             val_dict[fld_name] = fld_value
 

pydra/engine/helpers_file.py

@@ -579,7 +579,6 @@ def template_update(inputs, output_dir, state_ind=None, map_copyfiles=None):
     Should be run when all inputs used in the templates are already set.
 
     """
-
     inputs_dict_st = attr.asdict(inputs, recurse=False)
     if map_copyfiles is not None:
         inputs_dict_st.update(map_copyfiles)
@@ -654,7 +653,7 @@ def template_update_single(
         return inputs_dict_st[field.name]
     elif spec_type == "input" and inputs_dict_st[field.name] is False:
         # if input fld is set to False, the fld shouldn't be used (setting NOTHING)
-        return attr.NOTHING
+        return False
     else:  # inputs_dict[field.name] is True or spec_type is output
         value = _template_formatting(field, inputs, inputs_dict_st)
         # changing path so it is in the output_dir

pydra/engine/specs.py

@@ -13,6 +13,10 @@ def attr_fields(spec, exclude_names=()):
     return [field for field in spec.__attrs_attrs__ if field.name not in exclude_names]
 
 
+def attr_field(spec, name):
+    return [field for field in spec.__attrs_attrs__ if field.name == name][0]
+
+
 def attr_fields_dict(spec, exclude_names=()):
     return {
         field.name: field

pydra/engine/task.py

@@ -479,8 +479,12 @@ def _command_pos_args(self, field):
                     value = cmd_el_str
                 # if argstr has a more complex form, with "{input_field}"
                 if "{" in argstr and "}" in argstr:
-                    cmd_el_str = argstr.replace(f"{{{field.name}}}", str(value))
-                    cmd_el_str = argstr_formatting(cmd_el_str, self.inputs)
+                    # output_file_template and argstr should not be created when the value is False
+                    if not value and "output_file_template" in field.metadata:
+                        cmd_el_str = ""
+                    else:
+                        cmd_el_str = argstr.replace(f"{{{field.name}}}", str(value))
+                        cmd_el_str = argstr_formatting(cmd_el_str, self.inputs)
                 else:  # argstr has a simple form, e.g. "-f", or "--f"
                     if value:
                         cmd_el_str = f"{argstr} {value}"

pydra/engine/tests/test_shelltask_inputspec.py

@@ -1152,6 +1152,8 @@ def test_shell_cmd_inputs_template_6():
         executable="executable", input_spec=my_input_spec, inpA="inpA"
     )
     assert shelly.cmdline == f"executable inpA -o {str(shelly.output_dir / 'inpA_out')}"
+    # checking if the command is the same
+    assert shelly.cmdline == f"executable inpA -o {str(shelly.output_dir / 'inpA_out')}"
 
     # a string is provided for outA, so this should be used as the outA value
     shelly = ShellCommandTask(
@@ -1170,6 +1172,8 @@ def test_shell_cmd_inputs_template_6():
         executable="executable", input_spec=my_input_spec, inpA="inpA", outA=False
     )
     assert shelly.cmdline == "executable inpA"
+    # checking of the command is the same
+    assert shelly.cmdline == "executable inpA"
 
 
 def test_shell_cmd_inputs_template_6a():
@@ -1214,6 +1218,8 @@ def test_shell_cmd_inputs_template_6a():
         executable="executable", input_spec=my_input_spec, inpA="inpA"
     )
     assert shelly.cmdline == "executable inpA"
+    # checking if the command is the same
+    assert shelly.cmdline == "executable inpA"
 
     # a string is provided for outA, so this should be used as the outA value
     shelly = ShellCommandTask(
@@ -1232,6 +1238,58 @@ def test_shell_cmd_inputs_template_6a():
         executable="executable", input_spec=my_input_spec, inpA="inpA", outA=False
     )
     assert shelly.cmdline == "executable inpA"
+    # checking if the command is the same
+    assert shelly.cmdline == "executable inpA"
+
+
+def test_shell_cmd_inputs_template_6b():
+    """additional inputs with output_file_template that has type ty.Union[str, bool]
+    and default is set to False,
+    (using argstr in a format --argstr={})
+    """
+    my_input_spec = SpecInfo(
+        name="Input",
+        fields=[
+            (
+                "inpA",
+                attr.ib(
+                    type=str,
+                    metadata={
+                        "position": 1,
+                        "help_string": "inpA",
+                        "argstr": "",
+                        "mandatory": True,
+                    },
+                ),
+            ),
+            (
+                "outA",
+                attr.ib(
+                    type=ty.Union[str, bool],
+                    default=False,
+                    metadata={
+                        "position": 2,
+                        "help_string": "outA",
+                        "argstr": "--o={outA}",
+                        "output_file_template": "{inpA}_out",
+                    },
+                ),
+            ),
+        ],
+        bases=(ShellSpec,),
+    )
+
+    # no input for outA, but default is False, so the outA shouldn't be used
+    shelly = ShellCommandTask(
+        executable="executable", input_spec=my_input_spec, inpA="inpA"
+    )
+    assert shelly.cmdline == "executable inpA"
+
+    # a string is provided for outA, so this should be used as the outA value
+    shelly = ShellCommandTask(
+        executable="executable", input_spec=my_input_spec, inpA="inpA", outA="outA"
+    )
+    assert shelly.cmdline == "executable inpA --o=outA"
 
 
 def test_shell_cmd_inputs_template_7(tmpdir):
@@ -2080,7 +2138,7 @@ def test_shell_cmd_inputs_di(tmpdir, use_validator):
         == f"DenoiseImage -i {tmpdir.join('a_file.ext')} -s 1 -p 1 -r 2 -o [{str(shelly.output_dir / 'a_file_out.ext')}]"
     )
 
-    # input file name, noiseImage is set to True, so template is used in the output
+    # # input file name, noiseImage is set to True, so template is used in the output
     shelly = ShellCommandTask(
         executable="DenoiseImage",
         inputImageFilename=my_input_file,