ENH: Make --multi-step-reg a boolean action, enable by default

Author: mgxd

nibabies/cli/parser.py

@@ -15,7 +15,12 @@
 
 def _build_parser():
     """Build parser object."""
-    from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser
+    from argparse import (
+        Action,
+        ArgumentDefaultsHelpFormatter,
+        ArgumentParser,
+        BooleanOptionalAction,
+    )
     from functools import partial
     from pathlib import Path
 
@@ -759,7 +764,8 @@ def _str_none(val):
     )
     g_baby.add_argument(
         '--multi-step-reg',
-        action='store_true',
+        action=BooleanOptionalAction,
+        default=True,
         help='For certain adult templates (MNI152NLin6Asym), perform two step '
         'registrations (native -> MNIInfant -> template) and concatenate into a single xfm',
     )

nibabies/config.py

@@ -578,7 +578,7 @@ class workflow(_Config):
     """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
     medial_surface_nan = None
     """Fill medial surface with :abbr:`NaNs (not-a-number)` when sampling."""
-    multi_step_reg = False
+    multi_step_reg = True
     """Perform multiple registrations (native -> MNIInfant -> template) and concatenate into a
     single transform"""
     norm_csf = False

nibabies/workflows/tests/test_base.py

@@ -138,7 +138,7 @@ def _make_params(
     ignore: list[str] = None,
     bids_filters: dict = None,
     norm_csf: bool = False,
-    multi_step_reg: bool = False,
+    multi_step_reg: bool = True,
 ):
     if ignore is None:
         ignore = []
@@ -219,6 +219,7 @@ def _make_params(
         _make_params(bids_filters={'sbref': {'suffix': 'sbref'}}),
         _make_params(norm_csf=True),
         _make_params(multi_step_reg=True),
+        _make_params(multi_step_reg=False),
     ],
 )
 def test_init_nibabies_wf(