Merge pull request #466 from djarecka/fix/cmdline_sep_format

[fix] formatting cmdline for shelltask

Author: djarecka

pydra/engine/task.py

@@ -433,7 +433,7 @@ def _command_pos_args(self, field, state_ind, index):
                         argstr_f = argstr_formatting(
                             argstr, self.inputs, value_updates={field.name: val}
                         )
-                        argstr_formatted_l.append(argstr_f)
+                        argstr_formatted_l.append(f" {argstr_f}")
                     cmd_el_str = sep.join(argstr_formatted_l)
                 else:  # argstr has a simple form, e.g. "-f", or "--f"
                     cmd_el_str = sep.join([f" {argstr} {val}" for val in value])
@@ -445,7 +445,8 @@ def _command_pos_args(self, field, state_ind, index):
                     value = cmd_el_str
                 # if argstr has a more complex form, with "{input_field}"
                 if "{" in argstr and "}" in argstr:
-                    cmd_el_str = argstr_formatting(argstr, self.inputs)
+                    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

@@ -441,7 +441,35 @@ def test_shell_cmd_inputs_list_sep_2():
     assert shelly.cmdline == "executable -v aaa,bbb,ccc"
 
 
-def test_shell_cmd_inputs_sep_3():
+def test_shell_cmd_inputs_list_sep_2a():
+    """providing list as an additional input:, sep, and argstr with f-string"""
+    my_input_spec = SpecInfo(
+        name="Input",
+        fields=[
+            (
+                "inpA",
+                attr.ib(
+                    type=str,
+                    metadata={
+                        "position": 1,
+                        "help_string": "inpA",
+                        "sep": ",",
+                        "argstr": "-v {inpA}",
+                    },
+                ),
+            )
+        ],
+        bases=(ShellSpec,),
+    )
+
+    shelly = ShellCommandTask(
+        executable="executable", inpA=["aaa", "bbb", "ccc"], input_spec=my_input_spec
+    )
+    # a flag is used once
+    assert shelly.cmdline == "executable -v aaa,bbb,ccc"
+
+
+def test_shell_cmd_inputs_list_sep_3():
     """providing list as an additional input:, sep, argstr with ..."""
     my_input_spec = SpecInfo(
         name="Input",
@@ -469,6 +497,34 @@ def test_shell_cmd_inputs_sep_3():
     assert shelly.cmdline == "executable -v aaa, -v bbb, -v ccc"
 
 
+def test_shell_cmd_inputs_list_sep_3a():
+    """providing list as an additional input:, sep, argstr with ... and f-string"""
+    my_input_spec = SpecInfo(
+        name="Input",
+        fields=[
+            (
+                "inpA",
+                attr.ib(
+                    type=str,
+                    metadata={
+                        "position": 1,
+                        "help_string": "inpA",
+                        "sep": ",",
+                        "argstr": "-v {inpA}...",
+                    },
+                ),
+            )
+        ],
+        bases=(ShellSpec,),
+    )
+
+    shelly = ShellCommandTask(
+        executable="executable", inpA=["aaa", "bbb", "ccc"], input_spec=my_input_spec
+    )
+    # a flag is repeated
+    assert shelly.cmdline == "executable -v aaa, -v bbb, -v ccc"
+
+
 def test_shell_cmd_inputs_sep_4():
     """providing 1-el list as an additional input:, sep, argstr with ...,"""
     my_input_spec = SpecInfo(