Merge pull request #710 from satra/fix/reporting

Moved silly testing to autogeneration

Author: satra

Makefile

@@ -66,7 +66,12 @@ html:
 	@echo "building docs"
 	make -C doc clean html
 
-check-before-commit: trailing-spaces html test
+specs:
+	@echo "Checking specs and autogenerating spec tests"
+	python tools/checkspecs.py
+
+check-before-commit: trailing-spaces html test specs
 	@echo "removed spaces"
 	@echo "built docs"
 	@echo "ran test"
+	@echo "generated spec tests"

nipype/algorithms/modelgen.py

@@ -743,32 +743,3 @@ def _list_outputs(self):
             outputs['sparse_png_file'] = os.path.join(os.getcwd(), 'sparse.png')
             outputs['sparse_svg_file'] = os.path.join(os.getcwd(), 'sparse.svg')
         return outputs
-
-'''
-
-Need to figure out how this component will work!!! multiple inheritence is causing a big headache
-
-class SpecifySparseSPMModelInputSpec(SpecifySPMModelInputSpec, SpecifySparseModelInputSpec):
-    pass
-
-class SpecifySparseSPMModel(SpecifySparseModel, SpecifySPMModel):
-    """Combines SPM specific options with sparse options
-    """
-    input_spec = SpecifySparseSPMModelInputSpec
-    output_spec = SpecifySparseModelOutputSpec
-
-    def _generate_design(self, infolist=None):
-        raise Exception('not working yet')
-        if (self.inputs.input_units == 'scans') and (self.inputs.output_units == 'secs'):
-            if isdefined(self.inputs.volumes_in_cluster) and (self.inputs.volumes_in_cluster > 1):
-                raise NotImplementedError("Cannot scale timings if times are scans and acquisition is clustered")
-        if isdefined(self.inputs.subject_info):
-            infolist = self.inputs.subject_info
-        else:
-            infolist = gen_info(self.inputs.event_files)
-        clusterlist = self._generate_clustered_design(infolist)
-        if not isdefined(self.inputs.concatenate_runs):
-            super(SpecifySparseSPMModel, self)._generate_design(infolist=clusterlist)
-        else:
-            self._generate_spm_design(infolist=clusterlist)
-'''

nipype/algorithms/rapidart.py

@@ -266,8 +266,6 @@ class ArtifactDetect(BaseInterface):
     output_spec = ArtifactDetectOutputSpec
 
     def __init__(self, **inputs):
-        warn(('Deprecation warning: "bound_by_brainmask" will be set to True'
-              'in release 0.8'))
         super(ArtifactDetect, self).__init__(**inputs)
 
     def _get_output_filenames(self, motionfile, output_dir):

nipype/algorithms/tests/test_auto_AddCSVColumn.py

@@ -0,0 +1,24 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import AddCSVColumn
+def test_AddCSVColumn_inputs():
+    input_map = dict(extra_column_heading=dict(),
+    extra_field=dict(),
+    out_file=dict(usedefault=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    )
+    inputs = AddCSVColumn.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_AddCSVColumn_outputs():
+    output_map = dict(csv_file=dict(),
+    )
+    outputs = AddCSVColumn.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/algorithms/tests/test_auto_ArtifactDetect.py

@@ -0,0 +1,64 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.rapidart import ArtifactDetect
+def test_ArtifactDetect_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    plot_type=dict(usedefault=True,
+    ),
+    mask_type=dict(mandatory=True,
+    ),
+    mask_threshold=dict(),
+    parameter_source=dict(mandatory=True,
+    ),
+    translation_threshold=dict(mandatory=True,
+    xor=['norm_threshold'],
+    ),
+    global_threshold=dict(usedefault=True,
+    ),
+    bound_by_brainmask=dict(usedefault=True,
+    ),
+    realigned_files=dict(mandatory=True,
+    ),
+    rotation_threshold=dict(mandatory=True,
+    xor=['norm_threshold'],
+    ),
+    save_plot=dict(usedefault=True,
+    ),
+    use_differences=dict(minlen=2,
+    maxlen=2,
+    usedefault=True,
+    ),
+    norm_threshold=dict(mandatory=True,
+    xor=['rotation_threshold', 'translation_threshold'],
+    ),
+    zintensity_threshold=dict(mandatory=True,
+    ),
+    use_norm=dict(requires=['norm_threshold'],
+    usedefault=True,
+    ),
+    mask_file=dict(),
+    intersect_mask=dict(),
+    realignment_parameters=dict(mandatory=True,
+    ),
+    )
+    inputs = ArtifactDetect.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_ArtifactDetect_outputs():
+    output_map = dict(displacement_files=dict(),
+    outlier_files=dict(),
+    mask_files=dict(),
+    intensity_files=dict(),
+    norm_files=dict(),
+    statistic_files=dict(),
+    plot_files=dict(),
+    )
+    outputs = ArtifactDetect.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py

@@ -0,0 +1,22 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import CalculateNormalizedMoments
+def test_CalculateNormalizedMoments_inputs():
+    input_map = dict(moment=dict(mandatory=True,
+    ),
+    timeseries_file=dict(mandatory=True,
+    ),
+    )
+    inputs = CalculateNormalizedMoments.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_CalculateNormalizedMoments_outputs():
+    output_map = dict(moments=dict(),
+    )
+    outputs = CalculateNormalizedMoments.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/algorithms/tests/test_auto_CreateNifti.py

@@ -0,0 +1,26 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import CreateNifti
+def test_CreateNifti_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    data_file=dict(mandatory=True,
+    ),
+    affine=dict(),
+    header_file=dict(mandatory=True,
+    ),
+    )
+    inputs = CreateNifti.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_CreateNifti_outputs():
+    output_map = dict(nifti_file=dict(),
+    )
+    outputs = CreateNifti.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/algorithms/tests/test_auto_Distance.py

@@ -0,0 +1,31 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import Distance
+def test_Distance_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    volume1=dict(mandatory=True,
+    ),
+    method=dict(usedefault=True,
+    ),
+    mask_volume=dict(),
+    volume2=dict(mandatory=True,
+    ),
+    )
+    inputs = Distance.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_Distance_outputs():
+    output_map = dict(distance=dict(),
+    point2=dict(),
+    histogram=dict(),
+    point1=dict(),
+    )
+    outputs = Distance.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/algorithms/tests/test_auto_FuzzyOverlap.py

@@ -0,0 +1,33 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import FuzzyOverlap
+def test_FuzzyOverlap_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    weighting=dict(usedefault=True,
+    ),
+    in_tst=dict(mandatory=True,
+    ),
+    out_file=dict(usedefault=True,
+    ),
+    in_ref=dict(mandatory=True,
+    ),
+    )
+    inputs = FuzzyOverlap.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_FuzzyOverlap_outputs():
+    output_map = dict(class_fji=dict(),
+    class_fdi=dict(),
+    diff_file=dict(),
+    dice=dict(),
+    jaccard=dict(),
+    )
+    outputs = FuzzyOverlap.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/algorithms/tests/test_auto_Gunzip.py

@@ -0,0 +1,23 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import Gunzip
+def test_Gunzip_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    )
+    inputs = Gunzip.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_Gunzip_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = Gunzip.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value