Merge pull request #2941 from josephmje/master

[FIX] Remove '=' signs from EddyQuad argument specifications

Author: effigies

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/fsl/epi.py

@@ -1246,48 +1246,48 @@ class EddyQuadInputSpec(FSLCommandInputSpec):
     idx_file = File(
         exists=True,
         mandatory=True,
-        argstr="--eddyIdx=%s",
+        argstr="--eddyIdx %s",
         desc=("File containing indices for all volumes into acquisition "
               "parameters")
     )
     param_file = File(
         exists=True,
         mandatory=True,
-        argstr="--eddyParams=%s",
+        argstr="--eddyParams %s",
         desc="File containing acquisition parameters"
     )
     mask_file = File(
         exists=True,
         mandatory=True,
-        argstr="--mask=%s",
+        argstr="--mask %s",
         desc="Binary mask file"
     )
     bval_file = File(
         exists=True,
         mandatory=True,
-        argstr="--bvals=%s",
+        argstr="--bvals %s",
         desc="b-values file"
     )
     bvec_file = File(
         exists=True,
-        argstr="--bvecs=%s",
+        argstr="--bvecs %s",
         desc=("b-vectors file - only used when <base_name>.eddy_residuals "
               "file is present")
     )
     output_dir = traits.Str(
         name_template='%s.qc',
         name_source=['base_name'],
-        argstr='--output-dir=%s',
+        argstr='--output-dir %s',
         desc="Output directory - default = '<base_name>.qc'",
     )
     field = File(
         exists=True,
-        argstr='--field=%s',
+        argstr='--field %s',
         desc="TOPUP estimated field (in Hz)",
     )
     slice_spec = File(
         exists=True,
-        argstr='--slspec=%s',
+        argstr='--slspec %s',
         desc="Text file specifying slice/group acquisition",
     )
     verbose = traits.Bool(
@@ -1365,9 +1365,9 @@ class EddyQuad(FSLCommand):
     >>> quad.inputs.field      = 'fieldmap_phase_fslprepared.nii'
     >>> quad.inputs.verbose    = True
     >>> quad.cmdline
-    'eddy_quad eddy_corrected --bvals=bvals.scheme --bvecs=bvecs.scheme \
---field=fieldmap_phase_fslprepared.nii --eddyIdx=epi_index.txt \
---mask=epi_mask.nii --output-dir=eddy_corrected.qc --eddyParams=epi_acqp.txt \
+    'eddy_quad eddy_corrected --bvals bvals.scheme --bvecs bvecs.scheme \
+--field fieldmap_phase_fslprepared.nii --eddyIdx epi_index.txt \
+--mask epi_mask.nii --output-dir eddy_corrected.qc --eddyParams epi_acqp.txt \
 --verbose'
     >>> res = quad.run() # doctest: +SKIP
 

nipype/interfaces/fsl/tests/test_auto_EddyQuad.py

@@ -12,34 +12,34 @@ def test_EddyQuad_inputs():
             usedefault=True,
         ),
         bval_file=dict(
-            argstr='--bvals=%s',
+            argstr='--bvals %s',
             mandatory=True,
         ),
-        bvec_file=dict(argstr='--bvecs=%s', ),
+        bvec_file=dict(argstr='--bvecs %s', ),
         environ=dict(
             nohash=True,
             usedefault=True,
         ),
-        field=dict(argstr='--field=%s', ),
+        field=dict(argstr='--field %s', ),
         idx_file=dict(
-            argstr='--eddyIdx=%s',
+            argstr='--eddyIdx %s',
             mandatory=True,
         ),
         mask_file=dict(
-            argstr='--mask=%s',
+            argstr='--mask %s',
             mandatory=True,
         ),
         output_dir=dict(
-            argstr='--output-dir=%s',
+            argstr='--output-dir %s',
             name_source=['base_name'],
             name_template='%s.qc',
         ),
         output_type=dict(),
         param_file=dict(
-            argstr='--eddyParams=%s',
+            argstr='--eddyParams %s',
             mandatory=True,
         ),
-        slice_spec=dict(argstr='--slspec=%s', ),
+        slice_spec=dict(argstr='--slspec %s', ),
         verbose=dict(argstr='--verbose', ),
     )
     inputs = EddyQuad.input_spec()

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',