Fix defaults.

PennLINC · Oct 8, 2024 · dc59a95 · dc59a95
1 parent 627ba9f
commit dc59a95
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Showing 7 changed files with 8 additions and 9 deletions.
diff --git a/xcp_d/interfaces/ants.py b/xcp_d/interfaces/ants.py
@@ -25,7 +25,7 @@
 
 
 class _ConvertTransformFileInputSpec(CommandLineInputSpec):
-    dimension = traits.Enum((3, 2), default=3, usedefault=True, argstr="%d", position=0)
+    dimension = traits.Enum(3, 2, usedefault=True, argstr="%d", position=0)
     in_transform = traits.File(exists=True, argstr="%s", mandatory=True, position=1)
     out_transform = traits.File(
         argstr="%s",

diff --git a/xcp_d/interfaces/bids.py b/xcp_d/interfaces/bids.py
@@ -312,7 +312,7 @@ class _BIDSURIInputSpec(DynamicTraitedSpec):
     out_dir = traits.Str(mandatory=True, desc="Output directory")
     metadata = traits.Dict(desc="Metadata dictionary")
     field = traits.Str(
-        default="Sources",
+        "Sources",
         usedefault=True,
         desc="Field to use for BIDS URIs in metadata dict",
     )

diff --git a/xcp_d/interfaces/censoring.py b/xcp_d/interfaces/censoring.py
@@ -215,7 +215,7 @@ class _CensorInputSpec(BaseInterfaceInputSpec):
         ),
     )
     column = traits.Str(
-        default="framewise_displacement",
+        "framewise_displacement",
         usedefault=True,
         mandatory=False,
         desc="Column name in the temporal mask to use for censoring.",

diff --git a/xcp_d/interfaces/connectivity.py b/xcp_d/interfaces/connectivity.py
@@ -31,7 +31,7 @@ class _NiftiParcellateInputSpec(BaseInterfaceInputSpec):
     atlas = File(exists=True, mandatory=True, desc="atlas file")
     atlas_labels = File(exists=True, mandatory=True, desc="atlas labels file")
     min_coverage = traits.Float(
-        default=0.5,
+        0.5,
         usedefault=True,
         desc=(
             "Coverage threshold to apply to parcels. "

diff --git a/xcp_d/interfaces/plotting.py b/xcp_d/interfaces/plotting.py
@@ -529,7 +529,6 @@ class _SlicesDirInputSpec(FSLCommandInputSpec):
 
     out_extension = traits.Enum(
         (".gif", ".png", ".svg"),
-        default=".gif",
         usedefault=True,
         desc="Convenience parameter to let xcp_d select the extension.",
     )
@@ -670,10 +669,10 @@ class _PlotCiftiParcellationInputSpec(BaseInterfaceInputSpec):
         desc="Labels for the CIFTI files.",
     )
     out_file = File(
+        "plot.svg",
         exists=False,
         mandatory=False,
         desc="Output file.",
-        default="plot.svg",
         usedefault=True,
     )
     vmin = traits.Float(

diff --git a/xcp_d/interfaces/workbench.py b/xcp_d/interfaces/workbench.py
@@ -622,7 +622,7 @@ class _CiftiParcellateWorkbenchInputSpec(_WBCommandInputSpec):
         "MODE",
         "COUNT_NONZERO",
         position=12,
-        default="MEAN",
+        usedefault=True,
         argstr="-method %s",
         desc="Specify method of parcellation (default MEAN, or MODE if label data)",
     )
@@ -709,7 +709,7 @@ class _CiftiSurfaceResampleInputSpec(_WBCommandInputSpec):
             "The BARYCENTRIC method is generally recommended for anatomical surfaces, "
             "in order to minimize smoothing."
         ),
-        default="BARYCENTRIC",
+        usedefault=True,
     )
     out_file = File(
         name_source=["in_file"],

diff --git a/xcp_d/workflows/bold/outputs.py b/xcp_d/workflows/bold/outputs.py
@@ -615,7 +615,7 @@ def init_postproc_derivatives_wf(
                     run_without_submitting=True,
                     mem_gb=1,
                     name="make_ccorrs_meta_dict2",
-                    iterfield=["in1"],
+                    iterfield=["in1", "metadata"],
                 )
                 workflow.connect([
                     (inputnode, make_ccorrs_meta_dict2, [("atlas_files", "in1")]),