fix(traits): Replace deprecated traits.List$Sub with traits.List($Sub)

nipype/algorithms/rapidart.py

@@ -189,7 +189,8 @@ class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
         desc="Source of movement parameters",
         mandatory=True,
     )
-    use_differences = traits.ListBool(
+    use_differences = traits.List(
+        traits.Bool,
         [True, False],
         minlen=2,
         maxlen=2,

nipype/algorithms/tests/test_auto_ArtifactDetect.py

@@ -48,8 +48,6 @@ def test_ArtifactDetect_inputs():
             xor=["norm_threshold"],
         ),
         use_differences=dict(
-            maxlen=2,
-            minlen=2,
             usedefault=True,
         ),
         use_norm=dict(

nipype/interfaces/ants/segmentation.py

@@ -1328,7 +1328,8 @@ class JointFusionInputSpec(ANTSCommandInputSpec):
         usedefault=True,
         desc=("Constrain solution to non-negative weights."),
     )
-    patch_radius = traits.ListInt(
+    patch_radius = traits.List(
+        traits.Int,
         minlen=3,
         maxlen=3,
         argstr="-p %s",

nipype/interfaces/ants/tests/test_auto_JointFusion.py

@@ -70,8 +70,6 @@ def test_JointFusion_inputs():
         ),
         patch_radius=dict(
             argstr="-p %s",
-            maxlen=3,
-            minlen=3,
         ),
         retain_atlas_voting_images=dict(
             argstr="-f",

nipype/interfaces/base/__init__.py

@@ -7,7 +7,8 @@
 This module defines the API of all nipype interfaces.
 
 """
-from traits.trait_handlers import TraitDictObject, TraitListObject
+from traits.trait_dict_object import TraitDictObject
+from traits.trait_list_object import TraitListObject
 from traits.trait_errors import TraitError
 
 from .core import (

nipype/interfaces/base/specs.py

@@ -15,7 +15,8 @@
 from packaging.version import Version
 
 from traits.trait_errors import TraitError
-from traits.trait_handlers import TraitDictObject, TraitListObject
+from traits.trait_dict_object import TraitDictObject
+from traits.trait_list_object import TraitListObject
 from ...utils.filemanip import md5, hash_infile, hash_timestamp
 from .traits_extension import (
     traits,

nipype/interfaces/dipy/base.py

@@ -2,6 +2,7 @@
 
 import os.path as op
 import inspect
+from functools import partial
 import numpy as np
 from ..base import (
     traits,
@@ -109,15 +110,15 @@ def convert_to_traits_type(dipy_type, is_file=False):
     dipy_type = dipy_type.lower()
     is_mandatory = bool("optional" not in dipy_type)
     if "variable" in dipy_type and "str" in dipy_type:
-        return traits.ListStr, is_mandatory
+        return partial(traits.List, traits.Str), is_mandatory
     elif "variable" in dipy_type and "int" in dipy_type:
-        return traits.ListInt, is_mandatory
+        return partial(traits.List, traits.Int), is_mandatory
     elif "variable" in dipy_type and "float" in dipy_type:
-        return traits.ListFloat, is_mandatory
+        return partial(traits.List, traits.Float), is_mandatory
     elif "variable" in dipy_type and "bool" in dipy_type:
-        return traits.ListBool, is_mandatory
+        return partial(traits.List, traits.Bool), is_mandatory
     elif "variable" in dipy_type and "complex" in dipy_type:
-        return traits.ListComplex, is_mandatory
+        return partial(traits.List, traits.Complex), is_mandatory
     elif "str" in dipy_type and not is_file:
         return traits.Str, is_mandatory
     elif "str" in dipy_type and is_file:

nipype/interfaces/dipy/tests/test_base.py

@@ -16,7 +16,7 @@
 
 def test_convert_to_traits_type():
     Params = namedtuple("Params", "traits_type is_file")
-    Res = namedtuple("Res", "traits_type is_mandatory")
+    Res = namedtuple("Res", "traits_type subtype is_mandatory")
     l_entries = [
         Params("variable string", False),
         Params("variable int", False),
@@ -42,35 +42,38 @@ def test_convert_to_traits_type():
         Params("complex, optional", False),
     ]
     l_expected = [
-        Res(traits.ListStr, True),
-        Res(traits.ListInt, True),
-        Res(traits.ListFloat, True),
-        Res(traits.ListBool, True),
-        Res(traits.ListComplex, True),
-        Res(traits.ListInt, False),
-        Res(traits.ListStr, False),
-        Res(traits.ListFloat, False),
-        Res(traits.ListBool, False),
-        Res(traits.ListComplex, False),
-        Res(traits.Str, True),
-        Res(traits.Int, True),
-        Res(File, True),
-        Res(traits.Float, True),
-        Res(traits.Bool, True),
-        Res(traits.Complex, True),
-        Res(traits.Str, False),
-        Res(traits.Int, False),
-        Res(File, False),
-        Res(traits.Float, False),
-        Res(traits.Bool, False),
-        Res(traits.Complex, False),
+        Res(traits.List, traits.Str, True),
+        Res(traits.List, traits.Int, True),
+        Res(traits.List, traits.Float, True),
+        Res(traits.List, traits.Bool, True),
+        Res(traits.List, traits.Complex, True),
+        Res(traits.List, traits.Int, False),
+        Res(traits.List, traits.Str, False),
+        Res(traits.List, traits.Float, False),
+        Res(traits.List, traits.Bool, False),
+        Res(traits.List, traits.Complex, False),
+        Res(traits.Str, None, True),
+        Res(traits.Int, None, True),
+        Res(File, None, True),
+        Res(traits.Float, None, True),
+        Res(traits.Bool, None, True),
+        Res(traits.Complex, None, True),
+        Res(traits.Str, None, False),
+        Res(traits.Int, None, False),
+        Res(File, None, False),
+        Res(traits.Float, None, False),
+        Res(traits.Bool, None, False),
+        Res(traits.Complex, None, False),
     ]
 
     for entry, res in zip(l_entries, l_expected):
         traits_type, is_mandatory = convert_to_traits_type(
             entry.traits_type, entry.is_file
         )
-        assert traits_type == res.traits_type
+        trait_instance = traits_type()
+        assert isinstance(trait_instance, res.traits_type)
+        if res.subtype:
+            assert isinstance(trait_instance.inner_traits()[0].trait_type, res.subtype)
         assert is_mandatory == res.is_mandatory
 
     with pytest.raises(IOError):

nipype/interfaces/mrtrix3/preprocess.py

@@ -99,8 +99,9 @@ class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
         mandatory=True,
         desc="input DWI image",
     )
-    axes = traits.ListInt(
-        default_value=[0, 1],
+    axes = traits.List(
+        traits.Int,
+        [0, 1],
         usedefault=True,
         sep=",",
         minlen=2,

nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py

@@ -9,8 +9,6 @@ def test_MRDeGibbs_inputs():
         ),
         axes=dict(
             argstr="-axes %s",
-            maxlen=2,
-            minlen=2,
             sep=",",
             usedefault=True,
         ),

nipype/interfaces/spm/preprocess.py

@@ -273,7 +273,8 @@ class ApplyVDMInputSpec(SPMCommandInputSpec):
         desc="phase encode direction input data have been acquired with",
         usedefault=True,
     )
-    write_which = traits.ListInt(
+    write_which = traits.List(
+        traits.Int,
         [2, 1],
         field="roptions.which",
         minlen=2,
@@ -524,7 +525,8 @@ class RealignInputSpec(SPMCommandInputSpec):
         field="eoptions.wrap",
         desc="Check if interpolation should wrap in [x,y,z]",
     )
-    write_which = traits.ListInt(
+    write_which = traits.List(
+        traits.Int,
         [2, 1],
         field="roptions.which",
         minlen=2,
@@ -731,7 +733,8 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec):
             "maximization and smoothness maximization of the estimated field."
         ),
     )
-    est_reg_factor = traits.ListInt(
+    est_reg_factor = traits.List(
+        traits.Int,
         [100000],
         field="uweoptions.lambda",
         minlen=1,
@@ -769,7 +772,8 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec):
         field="uweoptions.rem",
         desc="Re-estimate movement parameters at each unwarping iteration.",
     )
-    est_num_of_iterations = traits.ListInt(
+    est_num_of_iterations = traits.List(
+        traits.Int,
         [5],
         field="uweoptions.noi",
         minlen=1,
@@ -783,7 +787,8 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec):
         usedefault=True,
         desc="Point in position space to perform Taylor-expansion around.",
     )
-    reslice_which = traits.ListInt(
+    reslice_which = traits.List(
+        traits.Int,
         [2, 1],
         field="uwroptions.uwwhich",
         minlen=2,

nipype/interfaces/spm/tests/test_auto_ApplyVDM.py

@@ -41,8 +41,6 @@ def test_ApplyVDM_inputs():
         ),
         write_which=dict(
             field="roptions.which",
-            maxlen=2,
-            minlen=2,
             usedefault=True,
         ),
         write_wrap=dict(

nipype/interfaces/spm/tests/test_auto_Realign.py

@@ -56,8 +56,6 @@ def test_Realign_inputs():
         ),
         write_which=dict(
             field="roptions.which",
-            maxlen=2,
-            minlen=2,
             usedefault=True,
         ),
         write_wrap=dict(

nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py

@@ -15,17 +15,13 @@ def test_RealignUnwarp_inputs():
         ),
         est_num_of_iterations=dict(
             field="uweoptions.noi",
-            maxlen=1,
-            minlen=1,
             usedefault=True,
         ),
         est_re_est_mov_par=dict(
             field="uweoptions.rem",
         ),
         est_reg_factor=dict(
             field="uweoptions.lambda",
-            maxlen=1,
-            minlen=1,
             usedefault=True,
         ),
         est_reg_order=dict(
@@ -80,8 +76,6 @@ def test_RealignUnwarp_inputs():
         ),
         reslice_which=dict(
             field="uwroptions.uwwhich",
-            maxlen=2,
-            minlen=2,
             usedefault=True,
         ),
         reslice_wrap=dict(