PR: FIX Check that file exists in basedir, not current dir

.zenodo.json

@@ -676,7 +676,13 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "Holland Bloorview Kids Rehabilitation Hospital",
+      "name": "Tilley II, Steven",
+      "orcid": "0000-0003-4853-5082"
     }
+
   ],
   "keywords": [
     "neuroimaging",

nipype/algorithms/tests/test_auto_ACompCor.py

@@ -25,8 +25,8 @@ def test_ACompCor_inputs():
         realigned_file=dict(mandatory=True, ),
         regress_poly_degree=dict(usedefault=True, ),
         repetition_time=dict(),
-        save_metadata=dict(),
-        save_pre_filter=dict(),
+        save_metadata=dict(usedefault=True, ),
+        save_pre_filter=dict(usedefault=True, ),
         use_regress_poly=dict(
             deprecated='0.15.0',
             new_name='pre_filter',

nipype/algorithms/tests/test_auto_TCompCor.py

@@ -26,8 +26,8 @@ def test_TCompCor_inputs():
         realigned_file=dict(mandatory=True, ),
         regress_poly_degree=dict(usedefault=True, ),
         repetition_time=dict(),
-        save_metadata=dict(),
-        save_pre_filter=dict(),
+        save_metadata=dict(usedefault=True, ),
+        save_pre_filter=dict(usedefault=True, ),
         use_regress_poly=dict(
             deprecated='0.15.0',
             new_name='pre_filter',

nipype/interfaces/afni/tests/test_auto_Cat.py

@@ -21,10 +21,9 @@ def test_Cat_inputs():
             usedefault=True,
         ),
         omitconst=dict(argstr='-nonconst', ),
-        out_cint=dict(
-            xor=[
-                'out_format', 'out_nice', 'out_double', 'out_fint', 'out_int'
-            ], ),
+        out_cint=dict(xor=[
+            'out_format', 'out_nice', 'out_double', 'out_fint', 'out_int'
+        ], ),
         out_double=dict(
             argstr='-d',
             xor=['out_format', 'out_nice', 'out_int', 'out_fint', 'out_cint'],

nipype/interfaces/ants/tests/test_auto_ANTS.py

@@ -57,8 +57,8 @@ def test_ANTS_inputs():
         regularization=dict(argstr='%s', ),
         regularization_deformation_field_sigma=dict(
             requires=['regularization'], ),
-        regularization_gradient_field_sigma=dict(
-            requires=['regularization'], ),
+        regularization_gradient_field_sigma=dict(requires=['regularization'
+                                                           ], ),
         smoothing_sigmas=dict(
             argstr='--gaussian-smoothing-sigmas %s',
             sep='x',

nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py

@@ -41,11 +41,10 @@ def test_AntsJointFusion_inputs():
             nohash=True,
             usedefault=True,
         ),
-        out_atlas_voting_weight_name_format=dict(
-            requires=[
-                'out_label_fusion', 'out_intensity_fusion_name_format',
-                'out_label_post_prob_name_format'
-            ], ),
+        out_atlas_voting_weight_name_format=dict(requires=[
+            'out_label_fusion', 'out_intensity_fusion_name_format',
+            'out_label_post_prob_name_format'
+        ], ),
         out_intensity_fusion_name_format=dict(argstr='', ),
         out_label_fusion=dict(
             argstr='%s',

nipype/interfaces/ants/tests/test_auto_Atropos.py

@@ -51,8 +51,8 @@ def test_Atropos_inputs():
         prior_probability_threshold=dict(requires=['prior_weighting'], ),
         prior_weighting=dict(),
         save_posteriors=dict(),
-        use_mixture_model_proportions=dict(
-            requires=['posterior_formulation'], ),
+        use_mixture_model_proportions=dict(requires=['posterior_formulation'
+                                                     ], ),
         use_random_seed=dict(
             argstr='--use-random-seed %d',
             usedefault=True,

nipype/interfaces/base/core.py

@@ -203,10 +203,10 @@ def _check_requires(self, spec, name, value):
             ]
             if any(values) and isdefined(value):
                 if len(values) > 1:
-                    fmt = ("%s requires values for inputs %s because '%s' is set. " 
+                    fmt = ("%s requires values for inputs %s because '%s' is set. "
                            "For a list of required inputs, see %s.help()")
                 else:
-                    fmt = ("%s requires a value for input %s because '%s' is set. " 
+                    fmt = ("%s requires a value for input %s because '%s' is set. "
                            "For a list of required inputs, see %s.help()")
                 msg = fmt % (self.__class__.__name__,
                              ', '.join("'%s'" % req for req in spec.requires),

nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py

@@ -33,11 +33,10 @@ def test_AccuracyTester_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_AccuracyTester_outputs():
-    output_map = dict(
-        output_directory=dict(
-            argstr='%s',
-            position=1,
-        ), )
+    output_map = dict(output_directory=dict(
+        argstr='%s',
+        position=1,
+    ), )
     outputs = AccuracyTester.output_spec()
 
     for key, metadata in list(output_map.items()):

nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py

@@ -22,12 +22,11 @@ def test_FeatureExtractor_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_FeatureExtractor_outputs():
-    output_map = dict(
-        mel_ica=dict(
-            argstr='%s',
-            copyfile=False,
-            position=-1,
-        ), )
+    output_map = dict(mel_ica=dict(
+        argstr='%s',
+        copyfile=False,
+        position=-1,
+    ), )
     outputs = FeatureExtractor.output_spec()
 
     for key, metadata in list(output_map.items()):

nipype/interfaces/fsl/tests/test_auto_TrainingSetCreator.py

@@ -4,24 +4,22 @@
 
 
 def test_TrainingSetCreator_inputs():
-    input_map = dict(
-        mel_icas_in=dict(
-            argstr='%s',
-            copyfile=False,
-            position=-1,
-        ), )
+    input_map = dict(mel_icas_in=dict(
+        argstr='%s',
+        copyfile=False,
+        position=-1,
+    ), )
     inputs = TrainingSetCreator.input_spec()
 
     for key, metadata in list(input_map.items()):
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_TrainingSetCreator_outputs():
-    output_map = dict(
-        mel_icas_out=dict(
-            argstr='%s',
-            copyfile=False,
-            position=-1,
-        ), )
+    output_map = dict(mel_icas_out=dict(
+        argstr='%s',
+        copyfile=False,
+        position=-1,
+    ), )
     outputs = TrainingSetCreator.output_spec()
 
     for key, metadata in list(output_map.items()):

nipype/interfaces/spm/tests/test_auto_Level1Design.py

@@ -10,6 +10,7 @@ def test_Level1Design_inputs():
             mandatory=True,
         ),
         factor_info=dict(field='fact', ),
+        flags=dict(),
         global_intensity_normalization=dict(field='global', ),
         interscan_interval=dict(
             field='timing.RT',

nipype/pipeline/engine/utils.py

@@ -486,7 +486,7 @@ def modify_paths(object, relative=True, basedir=None):
             out = tuple(out)
     else:
         if isdefined(object):
-            if isinstance(object, (str, bytes)) and os.path.isfile(object):
+            if isinstance(object, (str, bytes)) and os.path.isfile(os.path.join(basedir, object)):
                 if relative:
                     if config.getboolean('execution', 'use_relative_paths'):
                         out = relpath(object, start=basedir)