renamed additional_args to append_args

nipype · tclose · Apr 1, 2025 · Feb 23, 2025 · Feb 23, 2025 · Feb 23, 2025
commit ba08ee94e5c4466b1306f472338fc3344ff7539f
diff --git a/pydra/compose/shell/builder.py b/pydra/compose/shell/builder.py
@@ -210,7 +210,7 @@ def make(
         # Set positions for the remaining inputs that don't have an explicit position
         position_stack = remaining_positions(list(parsed_inputs.values()))
         for inpt in parsed_inputs.values():
-            if inpt.name == "additional_args":
+            if inpt.name == "append_args":
                 continue
             if inpt.position is None:
                 inpt.position = position_stack.pop(0)
@@ -544,11 +544,11 @@ def remaining_positions(
         If multiple fields have the same position
     """
     if num_args is None:
-        num_args = len(args) - 1  # Subtract 1 for the 'additional_args' field
+        num_args = len(args) - 1  # Subtract 1 for the 'append_args' field
     # Check for multiple positions
     positions = defaultdict(list)
     for arg in args:
-        if arg.name == "additional_args":
+        if arg.name == "append_args":
             continue
         if arg.position is not None:
             if arg.position >= 0:

diff --git a/pydra/compose/shell/task.py b/pydra/compose/shell/task.py
@@ -220,7 +220,7 @@ def _resolve_value(
 
 
 @state_array_support
-def additional_args_converter(value: ty.Any) -> list[str]:
+def append_args_converter(value: ty.Any) -> list[str]:
     """Convert additional arguments to a list of strings."""
     if isinstance(value, str):
         return shlex.split(value)
@@ -234,17 +234,17 @@ class ShellTask(base.Task[ShellOutputsType]):
 
     _task_type = "shell"
 
-    BASE_NAMES = ["additional_args"]
+    BASE_NAMES = ["append_args"]
 
     EXECUTABLE_HELP = (
         "the first part of the command, can be a string, "
         "e.g. 'ls', or a list, e.g. ['ls', '-l', 'dirname']"
     )
 
-    additional_args: list[str | File] = field.arg(
-        name="additional_args",
+    append_args: list[str | File] = field.arg(
+        name="append_args",
         default=attrs.Factory(list),
-        converter=additional_args_converter,
+        converter=append_args_converter,
         type=list[str | File],
         sep=" ",
         help="Additional free-form arguments to append to the end of the command.",
@@ -289,7 +289,7 @@ def _command_args(self, values: dict[str, ty.Any]) -> list[str]:
                 del values[fld.name]
         # Drop special fields that are added separately
         del values["executable"]
-        del values["additional_args"]
+        del values["append_args"]
         # Add executable
         pos_args = [
             self._command_shelltask_executable(fld, self.executable),
@@ -309,7 +309,7 @@ def _command_args(self, values: dict[str, ty.Any]) -> list[str]:
         # pos_args values are each a list of arguments, so concatenate lists after sorting
         command_args = sum(cmd_args, [])
         # Append additional arguments to the end of the command
-        command_args += self.additional_args
+        command_args += self.append_args
         return command_args
 
     def _command_shelltask_executable(

diff --git a/pydra/compose/shell/tests/test_shell_cmdline.py b/pydra/compose/shell/tests/test_shell_cmdline.py
@@ -34,7 +34,7 @@ class Outputs(shell.Outputs):
         inpA: str = shell.arg(position=1, help="inp1", argstr="")
 
     shelly = Shelly(
-        additional_args=["arg"],
+        append_args=["arg"],
         inpA="inp1",
     )
     assert shelly.cmdline == "executable inp1 arg"
@@ -52,7 +52,7 @@ class Outputs(shell.Outputs):
         inpA: str = shell.arg(help="inpA", argstr="")
 
     shelly = Shelly(
-        additional_args=["arg"],
+        append_args=["arg"],
         inpA="inpNone1",
     )
     # inp1 should be the first one after executable
@@ -72,7 +72,7 @@ class Outputs(shell.Outputs):
 
     # separate command into exec + args
     shelly = Shelly(
-        additional_args=["arg"],
+        append_args=["arg"],
         inpA="inp-1",
     )
     # inp1 should be last before arg
@@ -194,7 +194,7 @@ class Outputs(shell.Outputs):
         inpA: bool = shell.arg(position=1, help="inpA", argstr="-v")
 
     # separate command into exec + args
-    shelly = Shelly(additional_args=["arg"], inpA=True)
+    shelly = Shelly(append_args=["arg"], inpA=True)
     # a flag is used without any additional argument
     assert shelly.cmdline == "executable -v arg"
 

diff --git a/pydra/compose/shell/tests/test_shell_fields.py b/pydra/compose/shell/tests/test_shell_fields.py
@@ -34,7 +34,7 @@ def test_interface_template():
         ),
         shell.arg(name="in_path", type=FsObject, position=1),
         output,
-        shell.Task.additional_args,
+        shell.Task.append_args,
     ]
     assert sorted_fields(Cp.Outputs) == [
         output,
@@ -89,7 +89,7 @@ def test_interface_template_w_types_and_path_template_ext():
         ),
         shell.arg(name="in_image", type=image.Png, position=1),
         output,
-        shell.Task.additional_args,
+        shell.Task.append_args,
     ]
     assert sorted_fields(TrimPng.Outputs) == [
         output,
@@ -131,7 +131,7 @@ def test_interface_template_w_modify():
         shell.arg(
             name="image", type=image.Png, position=1, copy_mode=File.CopyMode.copy
         ),
-        shell.Task.additional_args,
+        shell.Task.append_args,
     ]
     assert sorted_fields(TrimPng.Outputs) == [
         shell.out(
@@ -216,7 +216,7 @@ def test_interface_template_more_complex():
             default=None,
             position=6,
         ),
-        shell.Task.additional_args,
+        shell.Task.append_args,
     ]
     assert sorted_fields(Cp.Outputs) == [
         output,
@@ -311,7 +311,7 @@ def test_interface_template_with_overrides_and_optionals():
             sep=" ",
             position=5,
         ),
-    ] + outargs + [shell.Task.additional_args]
+    ] + outargs + [shell.Task.append_args]
     assert sorted_fields(Cp.Outputs) == outargs + [
         shell.out(
             name="return_code",
@@ -374,7 +374,7 @@ def test_interface_template_with_defaults():
             position=6,
             sep=" ",
         ),
-        shell.Task.additional_args,
+        shell.Task.append_args,
     ]
     assert sorted_fields(Cp.Outputs) == [
         output,
@@ -444,7 +444,7 @@ def test_interface_template_with_type_overrides():
             position=6,
             sep=" ",
         ),
-        shell.Task.additional_args,
+        shell.Task.append_args,
     ]
     assert sorted_fields(Cp.Outputs) == [
         output,
@@ -584,7 +584,7 @@ class Outputs(shell.Outputs):
 def test_shell_fields(Ls):
     assert sorted([a.name for a in sorted_fields(Ls)]) == sorted(
         [
-            "additional_args",
+            "append_args",
             "executable",
             "directory",
             "hidden",
@@ -714,7 +714,7 @@ class Outputs(shell.Outputs):
             )
 
     assert sorted([a.name for a in attrs.fields(A) if not a.name.startswith("_")]) == [
-        "additional_args",
+        "append_args",
         "executable",
         "x",
         "y",
@@ -753,7 +753,7 @@ class Outputs(shell.Outputs):
             position=1,
         ),
         output,
-        shell.Task.additional_args,
+        shell.Task.append_args,
     ]
     assert sorted_fields(A.Outputs) == [
         output,
@@ -1011,7 +1011,7 @@ def test_shell_help1():
     ).split(
         "\n"
     ) + [
-        "- additional_args: list[str | generic/file]; default-factory = list()",
+        "- append_args: list[str | generic/file]; default-factory = list()",
         "    Additional free-form arguments to append to the end of the command.",
         "",
         "Outputs:",
@@ -1036,7 +1036,7 @@ def sorted_fields(interface):
     length = len(fields) - 1
 
     def pos_key(out: shell.out) -> int:
-        if out.name == "additional_args":
+        if out.name == "append_args":
             return (length + 1, out.name)
         try:
             pos = out.position

diff --git a/pydra/compose/shell/tests/test_shell_run.py b/pydra/compose/shell/tests/test_shell_run.py
@@ -78,7 +78,7 @@ def test_shell_cmd_2a(worker, results_function, tmp_path):
     cmd_exec = "echo"
     cmd_args = ["hail", "pydra"]
     # separate command into exec + args
-    shelly = shell.define(cmd_exec)(additional_args=cmd_args)
+    shelly = shell.define(cmd_exec)(append_args=cmd_args)
 
     assert shelly.executable == "echo"
     assert shelly.cmdline == "echo " + " ".join(cmd_args)
@@ -95,7 +95,7 @@ def test_shell_cmd_2b(worker, results_function, tmp_path):
     cmd_exec = "echo"
     cmd_args = ["pydra"]
     # separate command into exec + args
-    shelly = shell.define(cmd_exec)(additional_args=cmd_args)
+    shelly = shell.define(cmd_exec)(append_args=cmd_args)
 
     assert shelly.executable == "echo"
     assert shelly.cmdline == "echo pydra"
@@ -138,10 +138,10 @@ def test_shell_cmd_4(worker, tmp_path):
     cmd_exec = "echo"
     cmd_args = [["nipype"], ["pydra"]]
     # separate command into exec + args
-    shelly = shell.define(cmd_exec)().split(additional_args=cmd_args)
+    shelly = shell.define(cmd_exec)().split(append_args=cmd_args)
 
     assert shelly.executable == "echo"
-    assert shelly.additional_args == StateArray([["nipype"], ["pydra"]])
+    assert shelly.append_args == StateArray([["nipype"], ["pydra"]])
     # assert shelly.cmdline == ["echo nipype", "echo pydra"]
     outputs = shelly(worker=worker)
 
@@ -159,14 +159,10 @@ def test_shell_cmd_5(worker, tmp_path):
     cmd_exec = "echo"
     cmd_args = [["nipype"], ["pydra"]]
     # separate command into exec + args
-    shelly = (
-        shell.define(cmd_exec)()
-        .split(additional_args=cmd_args)
-        .combine("additional_args")
-    )
+    shelly = shell.define(cmd_exec)().split(append_args=cmd_args).combine("append_args")
 
     assert shelly.executable == "echo"
-    assert shelly.additional_args == StateArray([["nipype"], ["pydra"]])
+    assert shelly.append_args == StateArray([["nipype"], ["pydra"]])
     # assert shelly.cmdline == ["echo nipype", "echo pydra"]
     outputs = shelly(worker=worker)
 
@@ -182,11 +178,11 @@ def test_shell_cmd_6(worker, tmp_path):
     cmd_args = [["nipype"], ["pydra"]]
     # separate command into exec + args
     shelly = shell.define("shelly")().split(
-        ["executable", "additional_args"], executable=cmd_exec, additional_args=cmd_args
+        ["executable", "append_args"], executable=cmd_exec, append_args=cmd_args
     )
 
     assert shelly.executable == ["echo", ["echo", "-n"]]
-    assert shelly.additional_args == StateArray([["nipype"], ["pydra"]])
+    assert shelly.append_args == StateArray([["nipype"], ["pydra"]])
     outputs = shelly(cache_root=tmp_path, worker=worker)
 
     assert outputs.stdout == ["nipype\n", "pydra\n", "nipype", "pydra"]
@@ -217,15 +213,15 @@ def test_shell_cmd_7(worker, tmp_path):
     shelly = (
         shell.define("shelly")()
         .split(
-            ["executable", "additional_args"],
+            ["executable", "append_args"],
             executable=cmd_exec,
-            additional_args=cmd_args,
+            append_args=cmd_args,
         )
-        .combine("additional_args")
+        .combine("append_args")
     )
 
     assert shelly.executable == ["echo", ["echo", "-n"]]
-    assert shelly.additional_args == StateArray([["nipype"], ["pydra"]])
+    assert shelly.append_args == StateArray([["nipype"], ["pydra"]])
 
     outputs = shelly(worker=worker)
 
@@ -247,7 +243,7 @@ def StripAndListify(x: str) -> list[str]:
             return [x.strip()]
 
         listify = workflow.add(StripAndListify(x=shelly_pwd.stdout))
-        shelly_ls = workflow.add(shell.define(cmd2)(additional_args=listify.out))
+        shelly_ls = workflow.add(shell.define(cmd2)(append_args=listify.out))
         return shelly_ls.stdout
 
     wf = Workflow(cmd1="pwd", cmd2="ls")
@@ -285,9 +281,9 @@ class Outputs(shell.Outputs):
             pass
 
     # separate command into exec + args
-    shelly = Shelly(additional_args=cmd_args, opt_n=cmd_opt)
+    shelly = Shelly(append_args=cmd_args, opt_n=cmd_opt)
     assert shelly.executable == cmd_exec
-    assert shelly.additional_args == cmd_args
+    assert shelly.append_args == cmd_args
     assert shelly.cmdline == "echo -n 'hello from pydra'"
 
     outputs = results_function(shelly, worker=worker, cache_root=tmp_path)
@@ -323,9 +319,9 @@ class Outputs(shell.Outputs):
             pass
 
     # separate command into exec + args
-    shelly = Shelly(additional_args=cmd_args, opt_n=cmd_opt, opt_hello=cmd_opt_hello)
+    shelly = Shelly(append_args=cmd_args, opt_n=cmd_opt, opt_hello=cmd_opt_hello)
     assert shelly.executable == cmd_exec
-    assert shelly.additional_args == cmd_args
+    assert shelly.append_args == cmd_args
     assert shelly.cmdline == "echo -n HELLO 'from pydra'"
     outputs = results_function(shelly, worker=worker, cache_root=tmp_path)
     assert outputs.stdout == "HELLO from pydra"
@@ -2389,7 +2385,7 @@ class Outputs(shell.Outputs):
                 callable=get_stderr,
             )
 
-    shelly = Shelly().split(additional_args=args)
+    shelly = Shelly().split(append_args=args)
 
     outputs = results_function(shelly, worker=worker, cache_root=tmp_path)
     for index in range(2):

diff --git a/pydra/environments/tests/test_singularity.py b/pydra/environments/tests/test_singularity.py
@@ -73,7 +73,7 @@ def test_singularity_2a(worker, tmp_path):
     # separate command into exec + args
     image = "docker://alpine"
     Singu = shell.define(cmd_exec)
-    singu = Singu(additional_args=cmd_args)
+    singu = Singu(append_args=cmd_args)
     assert singu.cmdline == f"{cmd_exec} {' '.join(cmd_args)}"
 
     with Submitter(