updated to refactored pydra package

Author: tclose

generate.py

@@ -15,11 +15,11 @@
 import black.parsing
 from fileformats.core import FileSet
 from fileformats.medimage_mrtrix3 import ImageFormat, ImageIn, ImageOut, Tracks
-from pydra.design import shell
-from pydra.design.base import NO_DEFAULT
+from pydra.compose import shell
+from pydra.compose.base import NO_DEFAULT
 from pydra.utils.typing import MultiInputObj
 from pydra.utils import add_exc_note
-from pydra.engine.helpers import list_fields
+from pydra.utils.general import list_fields
 
 
 logger = logging.getLogger("pydra-auto-gen")
@@ -330,7 +330,7 @@ def auto_gen_test(cmd_name: str, output_dir: Path, log_errors: bool, pkg_version
 
     if cmd_name in XFAIL:
         code_str += (
-            f"""@pytest.mark.xfail(reason="Task {cmd_name} is known not pass yet")"""
+            f"""@pytest.mark.xfail(reason="Job {cmd_name} is known not pass yet")"""
         )
 
     code_str += f"""

pydra/tasks/mrtrix3/manual/mrcalc.py

@@ -3,8 +3,7 @@
 from enum import Enum
 from fileformats.generic import File, Directory  # noqa: F401
 from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
-from pydra.engine import specs
-from pydra.design import shell
+from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 
 
@@ -73,7 +72,7 @@ def operations_formatter(
     )
 
 
-class MrCalc(specs.ShellDef["MrCalc.Outputs"]):
+class MrCalc(shell.Task["MrCalc.Outputs"]):
     """This command will only compute per-voxel operations. Use 'mrmath' to compute
     summary statistics across images or along image axes.
 
@@ -290,7 +289,7 @@ class MrCalc(specs.ShellDef["MrCalc.Outputs"]):
         default=False,
     )
 
-    class Outputs(specs.ShellOutputs):
+    class Outputs(shell.Outputs):
         output: ImageOut = shell.outarg(
             argstr="",
             position=-1,