fixed auto tests and style

satra · satra · commit b2e83fb9e317 · 2017-03-06T20:39:01.000-05:00
diff --git a/README.rst b/README.rst
@@ -78,8 +78,8 @@ Support and Communication
 -------------------------
 
 If you have a problem or would like to ask a question about how to do something in Nipype please open an issue to
-`NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a 
-platform similar to StackOverflow but dedicated to neuroinformatics. 
+`NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a
+platform similar to StackOverflow but dedicated to neuroinformatics.
 
 To participate in the Nipype development related discussions please use the following mailing list::
 
diff --git a/nipype/algorithms/tests/test_auto_CompCor.py b/nipype/algorithms/tests/test_auto_CompCor.py
diff --git a/nipype/algorithms/tests/test_auto_ErrorMap.py b/nipype/algorithms/tests/test_auto_ErrorMap.py
diff --git a/nipype/algorithms/tests/test_auto_Overlap.py b/nipype/algorithms/tests/test_auto_Overlap.py
diff --git a/nipype/algorithms/tests/test_auto_TSNR.py b/nipype/algorithms/tests/test_auto_TSNR.py
diff --git a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py
@@ -11,7 +11,6 @@ def test_CreateJacobianDeterminantImage_inputs():
     position=1,
     ),
     doLogJacobian=dict(argstr='%d',
-    mandatory=False,
     position=3,
     ),
     environ=dict(nohash=True,
@@ -35,7 +34,6 @@ def test_CreateJacobianDeterminantImage_inputs():
     terminal_output=dict(nohash=True,
     ),
     useGeometric=dict(argstr='%d',
-    mandatory=False,
     position=4,
     ),
     )
diff --git a/nipype/interfaces/ants/utils.py b/nipype/interfaces/ants/utils.py
@@ -145,9 +145,9 @@ class CreateJacobianDeterminantImageInputSpec(ANTSCommandInputSpec):
     outputImage = File(argstr='%s', mandatory=True,
                          position=2,
                          desc='output filename')
-    doLogJacobian = traits.Enum(0, 1, argstr='%d', mandatory=False, position=3,
+    doLogJacobian = traits.Enum(0, 1, argstr='%d', position=3,
                           desc='return the log jacobian')
-    useGeometric = traits.Enum(0, 1, argstr='%d', mandatory=False, position=4,
+    useGeometric = traits.Enum(0, 1, argstr='%d', position=4,
                           desc='return the geometric jacobian')
 
 class CreateJacobianDeterminantImageOutputSpec(TraitedSpec):
diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py
@@ -49,7 +49,6 @@ class Level1DesignInputSpec(BaseInterfaceInputSpec):
               "{'dgamma': {'derivs': True}}"))
     orthogonalization = traits.Dict(traits.Int, traits.Dict(traits.Int,
         traits.Either(traits.Bool,traits.Int)),
-        mandatory=False,
         desc=("which regressors to make orthogonal e.g., "
               "{1: {0:0,1:0,2:0}, 2: {0:1,1:1,2:0}} to make the second "
               "regressor in a 2-regressor model orthogonal to the first."),
diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
@@ -751,7 +751,7 @@ class FNIRTInputSpec(FSLCommandInputSpec):
     inwarp_file = File(exists=True, argstr='--inwarp=%s',
                        desc='name of file containing initial non-linear warps')
     in_intensitymap_file = traits.List(File(exists=True), argstr='--intin=%s',
-                                       copyfiles=False, minlen=1, maxlen=2,
+                                       copyfile=False, minlen=1, maxlen=2,
                                        desc=('name of file/files containing '
                                              'initial intensity mapping '
                                              'usually generated by previous '
diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py
@@ -1,9 +1,9 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from __future__ import unicode_literals
-from ..preprocess import ApplyXFM
+from ..preprocess import ApplyXfm
 
 
-def test_ApplyXFM_inputs():
+def test_ApplyXfm_inputs():
     input_map = dict(angle_rep=dict(argstr='-anglerep %s',
     ),
     apply_isoxfm=dict(argstr='-applyisoxfm %f',
@@ -145,19 +145,19 @@ def test_ApplyXFM_inputs():
     min_ver='5.0.0',
     ),
     )
-    inputs = ApplyXFM.input_spec()
+    inputs = ApplyXfm.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_ApplyXFM_outputs():
+def test_ApplyXfm_outputs():
     output_map = dict(out_file=dict(),
     out_log=dict(),
     out_matrix_file=dict(),
     )
-    outputs = ApplyXFM.output_spec()
+    outputs = ApplyXfm.output_spec()
 
     for key, metadata in list(output_map.items()):
         for metakey, value in list(metadata.items()):
diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py
@@ -48,7 +48,7 @@ def test_FNIRT_inputs():
     sep=',',
     ),
     in_intensitymap_file=dict(argstr='--intin=%s',
-    copyfiles=False,
+    copyfile=False,
     ),
     inmask_file=dict(argstr='--inmask=%s',
     ),
diff --git a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py
@@ -14,8 +14,7 @@ def test_Level1Design_inputs():
     ),
     model_serial_correlations=dict(mandatory=True,
     ),
-    orthogonalization=dict(mandatory=False,
-    ),
+    orthogonalization=dict(),
     session_info=dict(mandatory=True,
     ),
     )
diff --git a/nipype/interfaces/fsl/tests/test_maths.py b/nipype/interfaces/fsl/tests/test_maths.py
@@ -12,7 +12,7 @@
 from nipype.interfaces.fsl import no_fsl
 
 import pytest
-from nipype.testing.fixtures import create_files_in_directory_plus_output_type 
+from nipype.testing.fixtures import create_files_in_directory_plus_output_type
 
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
diff --git a/nipype/pipeline/engine/tests/test_engine.py b/nipype/pipeline/engine/tests/test_engine.py
@@ -326,14 +326,14 @@ def test_doubleconnect():
     flow1 = pe.Workflow(name='test')
     flow1.connect(a, 'a', b, 'a')
     x = lambda: flow1.connect(a, 'b', b, 'a')
-    with pytest.raises(Exception) as excinfo: 
+    with pytest.raises(Exception) as excinfo:
         x()
     assert "Trying to connect" in str(excinfo.value)
 
     c = pe.Node(IdentityInterface(fields=['a', 'b']), name='c')
     flow1 = pe.Workflow(name='test2')
     x = lambda: flow1.connect([(a, c, [('b', 'b')]), (b, c, [('a', 'b')])])
-    with pytest.raises(Exception) as excinfo: 
+    with pytest.raises(Exception) as excinfo:
         x()
     assert "Trying to connect" in str(excinfo.value)
 
@@ -481,7 +481,7 @@ def func1(in1):
                  name='n1')
     n2.inputs.in1 = [[1, [2]], 3, [4, 5]]
 
-    with pytest.raises(Exception) as excinfo: 
+    with pytest.raises(Exception) as excinfo:
         n2.run()
     assert "can only concatenate list" in str(excinfo.value)
 
@@ -518,7 +518,7 @@ def func2(a):
     # create dummy distributed plugin class
     from nipype.pipeline.plugins.base import DistributedPluginBase
 
-    # create a custom exception 
+    # create a custom exception
     class EngineTestException(Exception):
         pass
 
@@ -529,7 +529,7 @@ def _submit_job(self, node, updatehash=False):
     # check if a proper exception is raised
     with pytest.raises(EngineTestException) as excinfo:
         w1.run(plugin=RaiseError())
-    assert 'Submit called' == str(excinfo.value)        
+    assert 'Submit called' == str(excinfo.value)
 
     # rerun to ensure we have outputs
     w1.run(plugin='Linear')
@@ -539,7 +539,7 @@ def _submit_job(self, node, updatehash=False):
                               'crashdump_dir': wd}
 
     w1.run(plugin=RaiseError())
-    
+
 
 def test_old_config(tmpdir):
     wd = str(tmpdir)
@@ -607,7 +607,7 @@ def func1(in1):
     w1.config['execution'].update(**{'stop_on_first_rerun': True})
 
     w1.run()
-   
+
 
 def test_parameterize_dirs_false(tmpdir):
     from ....interfaces.utility import IdentityInterface
@@ -665,7 +665,7 @@ def func1(in1):
 
     # test running the workflow on serial conditions
     w1.run(plugin='MultiProc')
-    
+
 
 def test_write_graph_runs(tmpdir):
     os.chdir(str(tmpdir))
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
@@ -306,7 +306,7 @@ def touch(fname):
     else:
         assert False, "Should raise OSError on missing dependency"
 
-    shutil.rmtree(tmpdir)   
+    shutil.rmtree(tmpdir)
 
 
 def test_json():
