Merge pull request #1167 from chrisfilo/enh/nipype_cmd_multipath

Added support for lists of files as command line inputs.

Author: satra

nipype/utils/nipype_cmd.py

@@ -2,7 +2,7 @@
 import argparse
 import inspect
 import sys
-from nipype.interfaces.base import Interface
+from nipype.interfaces.base import Interface, InputMultiPath
 from nipype.utils.misc import str2bool
 
 def listClasses(module=None):
@@ -23,11 +23,17 @@ def add_options(parser=None, module=None, function=None):
         inputs = interface.input_spec()
         for name, spec in sorted(interface.inputs.traits(transient=None).items()):
             desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:]
+            args = {}
+            
             if hasattr(spec, "mandatory") and spec.mandatory:
-                parser.add_argument(name, help=desc)
+                if spec.is_trait_type(InputMultiPath):
+                    args["nargs"]="+"
+                parser.add_argument(name, help=desc, **args)
             else:
+                if spec.is_trait_type(InputMultiPath):
+                    args["nargs"]="*"
                 parser.add_argument("--%s"%name, dest=name,
-                                    help=desc)
+                                    help=desc, **args)
     return parser, interface
 
 def run_instance(interface, options):

nipype/utils/tests/test_cmd.py

@@ -83,15 +83,16 @@ def test_run_4d_realign_without_arguments(self):
 
         self.assertEqual(stderr.getvalue(),
 """usage: nipype_cmd nipype.interfaces.nipy FmriRealign4d [-h]
-                                                       [--between_loops BETWEEN_LOOPS]
+                                                       [--between_loops [BETWEEN_LOOPS [BETWEEN_LOOPS ...]]]
                                                        [--ignore_exception IGNORE_EXCEPTION]
-                                                       [--loops LOOPS]
+                                                       [--loops [LOOPS [LOOPS ...]]]
                                                        [--slice_order SLICE_ORDER]
-                                                       [--speedup SPEEDUP]
+                                                       [--speedup [SPEEDUP [SPEEDUP ...]]]
                                                        [--start START]
                                                        [--time_interp TIME_INTERP]
                                                        [--tr_slices TR_SLICES]
-                                                       in_file tr
+                                                       in_file [in_file ...]
+                                                       tr
 nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments
 """)
         self.assertEqual(stdout.getvalue(), '')