fix: Narrowly quote %s argstrs with File/Directory traits

Author: effigies

nipype/interfaces/base/core.py

@@ -32,7 +32,7 @@
 
 from ...external.due import due
 
-from .traits_extension import traits, isdefined, Undefined
+from .traits_extension import traits, isdefined, BasePath, Undefined
 from .specs import (
     BaseInterfaceInputSpec,
     CommandLineInputSpec,
@@ -798,6 +798,13 @@ def _format_arg(self, name, trait_spec, value):
             # type-checking code here as well
             sep = trait_spec.sep if trait_spec.sep is not None else " "
 
+            if argstr == '%s':
+                inner_traits = getattr(trait_spec, "inner_traits", None)
+                if inner_traits and any(
+                    t.is_trait_type(BasePath) for t in inner_traits
+                ):
+                    values = [shlex.quote(elt) for elt in value]
+
             if argstr.endswith("..."):
                 # repeatable option
                 # --id %d... will expand to
@@ -807,6 +814,8 @@ def _format_arg(self, name, trait_spec, value):
             else:
                 return argstr % sep.join(str(elt) for elt in value)
         else:
+            if argstr == '%s' and trait_spec.is_trait_type(BasePath):
+                return shlex.quote(value)
             # Append options using format string.
             return argstr % value