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MAINT: Various minor improvements to complement previous PR #2964

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merged 7 commits into from
Jul 17, 2019
Merged

MAINT: Various minor improvements to complement previous PR #2964

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e848165
sty: clarity suggestions from @mgxd
oesteban Jul 17, 2019
114ddf8
sty: pep257 and other stylistic changes to AFNI interfaces
oesteban Jul 17, 2019
406ab58
fix: make specs (updated extensions metadata for Files)
oesteban Jul 17, 2019
d29ea7b
fix: error in Makefile
oesteban Jul 17, 2019
0052814
sty: further pep257 changes
oesteban Jul 17, 2019
8bee7e6
Update nipype/interfaces/afni/preprocess.py [skip ci]
oesteban Jul 17, 2019
9257f75
sty: break lines in desc, do not escape quote marks [skip ci]
oesteban Jul 17, 2019
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -56,7 +56,7 @@ inplace:
$(PYTHON) setup.py build_ext -i

test-code: in
py.test --doctest-module nipype
py.test --doctest-modules nipype

test-coverage: clean-tests in
py.test --doctest-modules --cov-config .coveragerc --cov=nipype nipype
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11 changes: 7 additions & 4 deletions nipype/algorithms/tests/test_auto_ACompCor.py
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Expand Up @@ -22,7 +22,10 @@ def test_ACompCor_inputs():
),
num_components=dict(xor=['variance_threshold'], ),
pre_filter=dict(usedefault=True, ),
realigned_file=dict(mandatory=True, ),
realigned_file=dict(
extensions=None,
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In the spec tests, only explicitly specified metadata has gone in, previously. Why is extensions different?

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This is an oversight from the previous PR - 6c3858a#diff-07934241447dd5e65f51347e36fdd1ffR291

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Right. But, for example, exists=False is not in all of these, even though that's the default. Why is extensions=<default> in here? Is this something we can fix in the trait, instead?

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We could (and it was like that before that commit) replicate the same behavior of exists. Namely, the metadata is not propagated up to the base classes. I'm clueless about the implications of this.

For exists I just kept the original behavior.

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i think the intent was not so much to track the defaults of the class, but keywords that the user put in explicitly.

i do agree that these underlying metadata (if changed internally in traits_extension) will change the behavior of interfaces and it would be good to catch them. another side note, is how we deal with and improve pickled crashfile compatibility.

if we keep old behavior, then we must commit to not changing underlying defaults in traits_extension in the future.

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@satra Just to clarify, adding extensions metadata to everything is preferable?

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@effigies - if we do want to take note of underlying metadata changes, we either write a set of tests for each trait type that's used in nipype, and not add the defaults to these auto-tests.

or we simply pull every default into the auto test. more generally though, my hope is that we can move closer to the kind of testing we are planning to do with the afni folks. also start splitting interfaces into their own packages.

so for now, i think this ok. but we should think this through/generalize our goals a bit better.

mandatory=True,
),
regress_poly_degree=dict(usedefault=True, ),
repetition_time=dict(),
save_metadata=dict(usedefault=True, ),
Expand All @@ -40,9 +43,9 @@ def test_ACompCor_inputs():
assert getattr(inputs.traits()[key], metakey) == value
def test_ACompCor_outputs():
output_map = dict(
components_file=dict(),
metadata_file=dict(),
pre_filter_file=dict(),
components_file=dict(extensions=None, ),
metadata_file=dict(extensions=None, ),
pre_filter_file=dict(extensions=None, ),
)
outputs = ACompCor.output_spec()

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6 changes: 3 additions & 3 deletions nipype/algorithms/tests/test_auto_ActivationCount.py
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Expand Up @@ -15,9 +15,9 @@ def test_ActivationCount_inputs():
assert getattr(inputs.traits()[key], metakey) == value
def test_ActivationCount_outputs():
output_map = dict(
acm_neg=dict(),
acm_pos=dict(),
out_file=dict(),
acm_neg=dict(extensions=None, ),
acm_pos=dict(extensions=None, ),
out_file=dict(extensions=None, ),
)
outputs = ActivationCount.output_spec()

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12 changes: 9 additions & 3 deletions nipype/algorithms/tests/test_auto_AddCSVColumn.py
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Expand Up @@ -7,16 +7,22 @@ def test_AddCSVColumn_inputs():
input_map = dict(
extra_column_heading=dict(),
extra_field=dict(),
in_file=dict(mandatory=True, ),
out_file=dict(usedefault=True, ),
in_file=dict(
extensions=None,
mandatory=True,
),
out_file=dict(
extensions=None,
usedefault=True,
),
)
inputs = AddCSVColumn.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_AddCSVColumn_outputs():
output_map = dict(csv_file=dict(), )
output_map = dict(csv_file=dict(extensions=None, ), )
outputs = AddCSVColumn.output_spec()

for key, metadata in list(output_map.items()):
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2 changes: 1 addition & 1 deletion nipype/algorithms/tests/test_auto_AddCSVRow.py
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Expand Up @@ -14,7 +14,7 @@ def test_AddCSVRow_inputs():
for metakey, value in list(metadata.items()):
assert getattr(inputs.traits()[key], metakey) == value
def test_AddCSVRow_outputs():
output_map = dict(csv_file=dict(), )
output_map = dict(csv_file=dict(extensions=None, ), )
outputs = AddCSVRow.output_spec()

for key, metadata in list(output_map.items()):
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11 changes: 7 additions & 4 deletions nipype/algorithms/tests/test_auto_AddNoise.py
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Expand Up @@ -13,9 +13,12 @@ def test_AddNoise_inputs():
mandatory=True,
usedefault=True,
),
in_file=dict(mandatory=True, ),
in_mask=dict(),
out_file=dict(),
in_file=dict(
extensions=None,
mandatory=True,
),
in_mask=dict(extensions=None, ),
out_file=dict(extensions=None, ),
snr=dict(usedefault=True, ),
)
inputs = AddNoise.input_spec()
Expand All @@ -24,7 +27,7 @@ def test_AddNoise_inputs():
for metakey, value in list(metadata.items()):
assert getattr(inputs.traits()[key], metakey) == value
def test_AddNoise_outputs():
output_map = dict(out_file=dict(), )
output_map = dict(out_file=dict(extensions=None, ), )
outputs = AddNoise.output_spec()

for key, metadata in list(output_map.items()):
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2 changes: 1 addition & 1 deletion nipype/algorithms/tests/test_auto_ArtifactDetect.py
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Expand Up @@ -8,7 +8,7 @@ def test_ArtifactDetect_inputs():
bound_by_brainmask=dict(usedefault=True, ),
global_threshold=dict(usedefault=True, ),
intersect_mask=dict(usedefault=True, ),
mask_file=dict(),
mask_file=dict(extensions=None, ),
mask_threshold=dict(),
mask_type=dict(mandatory=True, ),
norm_threshold=dict(
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5 changes: 4 additions & 1 deletion nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py
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Expand Up @@ -6,7 +6,10 @@
def test_CalculateNormalizedMoments_inputs():
input_map = dict(
moment=dict(mandatory=True, ),
timeseries_file=dict(mandatory=True, ),
timeseries_file=dict(
extensions=None,
mandatory=True,
),
)
inputs = CalculateNormalizedMoments.input_spec()

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24 changes: 15 additions & 9 deletions nipype/algorithms/tests/test_auto_ComputeDVARS.py
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Expand Up @@ -8,8 +8,14 @@ def test_ComputeDVARS_inputs():
figdpi=dict(usedefault=True, ),
figformat=dict(usedefault=True, ),
figsize=dict(usedefault=True, ),
in_file=dict(mandatory=True, ),
in_mask=dict(mandatory=True, ),
in_file=dict(
extensions=None,
mandatory=True,
),
in_mask=dict(
extensions=None,
mandatory=True,
),
intensity_normalization=dict(usedefault=True, ),
remove_zerovariance=dict(usedefault=True, ),
save_all=dict(usedefault=True, ),
Expand All @@ -29,13 +35,13 @@ def test_ComputeDVARS_outputs():
avg_nstd=dict(),
avg_std=dict(),
avg_vxstd=dict(),
fig_nstd=dict(),
fig_std=dict(),
fig_vxstd=dict(),
out_all=dict(),
out_nstd=dict(),
out_std=dict(),
out_vxstd=dict(),
fig_nstd=dict(extensions=None, ),
fig_std=dict(extensions=None, ),
fig_vxstd=dict(extensions=None, ),
out_all=dict(extensions=None, ),
out_nstd=dict(extensions=None, ),
out_std=dict(extensions=None, ),
out_vxstd=dict(extensions=None, ),
)
outputs = ComputeDVARS.output_spec()

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24 changes: 18 additions & 6 deletions nipype/algorithms/tests/test_auto_ComputeMeshWarp.py
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Expand Up @@ -6,10 +6,22 @@
def test_ComputeMeshWarp_inputs():
input_map = dict(
metric=dict(usedefault=True, ),
out_file=dict(usedefault=True, ),
out_warp=dict(usedefault=True, ),
surface1=dict(mandatory=True, ),
surface2=dict(mandatory=True, ),
out_file=dict(
extensions=None,
usedefault=True,
),
out_warp=dict(
extensions=None,
usedefault=True,
),
surface1=dict(
extensions=None,
mandatory=True,
),
surface2=dict(
extensions=None,
mandatory=True,
),
weighting=dict(usedefault=True, ),
)
inputs = ComputeMeshWarp.input_spec()
Expand All @@ -20,8 +32,8 @@ def test_ComputeMeshWarp_inputs():
def test_ComputeMeshWarp_outputs():
output_map = dict(
distance=dict(),
out_file=dict(),
out_warp=dict(),
out_file=dict(extensions=None, ),
out_warp=dict(extensions=None, ),
)
outputs = ComputeMeshWarp.output_spec()

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12 changes: 9 additions & 3 deletions nipype/algorithms/tests/test_auto_CreateNifti.py
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Expand Up @@ -6,16 +6,22 @@
def test_CreateNifti_inputs():
input_map = dict(
affine=dict(),
data_file=dict(mandatory=True, ),
header_file=dict(mandatory=True, ),
data_file=dict(
extensions=None,
mandatory=True,
),
header_file=dict(
extensions=None,
mandatory=True,
),
)
inputs = CreateNifti.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_CreateNifti_outputs():
output_map = dict(nifti_file=dict(), )
output_map = dict(nifti_file=dict(extensions=None, ), )
outputs = CreateNifti.output_spec()

for key, metadata in list(output_map.items()):
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14 changes: 10 additions & 4 deletions nipype/algorithms/tests/test_auto_Distance.py
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Expand Up @@ -5,10 +5,16 @@

def test_Distance_inputs():
input_map = dict(
mask_volume=dict(),
mask_volume=dict(extensions=None, ),
method=dict(usedefault=True, ),
volume1=dict(mandatory=True, ),
volume2=dict(mandatory=True, ),
volume1=dict(
extensions=None,
mandatory=True,
),
volume2=dict(
extensions=None,
mandatory=True,
),
)
inputs = Distance.input_spec()

Expand All @@ -18,7 +24,7 @@ def test_Distance_inputs():
def test_Distance_outputs():
output_map = dict(
distance=dict(),
histogram=dict(),
histogram=dict(extensions=None, ),
point1=dict(),
point2=dict(),
)
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19 changes: 14 additions & 5 deletions nipype/algorithms/tests/test_auto_FramewiseDisplacement.py
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Expand Up @@ -7,10 +7,19 @@ def test_FramewiseDisplacement_inputs():
input_map = dict(
figdpi=dict(usedefault=True, ),
figsize=dict(usedefault=True, ),
in_file=dict(mandatory=True, ),
in_file=dict(
extensions=None,
mandatory=True,
),
normalize=dict(usedefault=True, ),
out_figure=dict(usedefault=True, ),
out_file=dict(usedefault=True, ),
out_figure=dict(
extensions=None,
usedefault=True,
),
out_file=dict(
extensions=None,
usedefault=True,
),
parameter_source=dict(mandatory=True, ),
radius=dict(usedefault=True, ),
save_plot=dict(usedefault=True, ),
Expand All @@ -24,8 +33,8 @@ def test_FramewiseDisplacement_inputs():
def test_FramewiseDisplacement_outputs():
output_map = dict(
fd_average=dict(),
out_figure=dict(),
out_file=dict(),
out_figure=dict(extensions=None, ),
out_file=dict(extensions=None, ),
)
outputs = FramewiseDisplacement.output_spec()

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7 changes: 5 additions & 2 deletions nipype/algorithms/tests/test_auto_FuzzyOverlap.py
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Expand Up @@ -5,10 +5,13 @@

def test_FuzzyOverlap_inputs():
input_map = dict(
in_mask=dict(),
in_mask=dict(extensions=None, ),
in_ref=dict(mandatory=True, ),
in_tst=dict(mandatory=True, ),
out_file=dict(usedefault=True, ),
out_file=dict(
extensions=None,
usedefault=True,
),
weighting=dict(usedefault=True, ),
)
inputs = FuzzyOverlap.input_spec()
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8 changes: 6 additions & 2 deletions nipype/algorithms/tests/test_auto_Gunzip.py
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Expand Up @@ -4,14 +4,18 @@


def test_Gunzip_inputs():
input_map = dict(in_file=dict(mandatory=True, ), )
input_map = dict(
in_file=dict(
extensions=None,
mandatory=True,
), )
inputs = Gunzip.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_Gunzip_outputs():
output_map = dict(out_file=dict(), )
output_map = dict(out_file=dict(extensions=None, ), )
outputs = Gunzip.output_spec()

for key, metadata in list(output_map.items()):
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11 changes: 7 additions & 4 deletions nipype/algorithms/tests/test_auto_ICC.py
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Expand Up @@ -5,7 +5,10 @@

def test_ICC_inputs():
input_map = dict(
mask=dict(mandatory=True, ),
mask=dict(
extensions=None,
mandatory=True,
),
subjects_sessions=dict(mandatory=True, ),
)
inputs = ICC.input_spec()
Expand All @@ -15,9 +18,9 @@ def test_ICC_inputs():
assert getattr(inputs.traits()[key], metakey) == value
def test_ICC_outputs():
output_map = dict(
icc_map=dict(),
session_var_map=dict(),
subject_var_map=dict(),
icc_map=dict(extensions=None, ),
session_var_map=dict(extensions=None, ),
subject_var_map=dict(extensions=None, ),
)
outputs = ICC.output_spec()

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5 changes: 4 additions & 1 deletion nipype/algorithms/tests/test_auto_Matlab2CSV.py
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Expand Up @@ -5,7 +5,10 @@

def test_Matlab2CSV_inputs():
input_map = dict(
in_file=dict(mandatory=True, ),
in_file=dict(
extensions=None,
mandatory=True,
),
reshape_matrix=dict(usedefault=True, ),
)
inputs = Matlab2CSV.input_spec()
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7 changes: 5 additions & 2 deletions nipype/algorithms/tests/test_auto_MergeCSVFiles.py
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Expand Up @@ -9,7 +9,10 @@ def test_MergeCSVFiles_inputs():
extra_column_heading=dict(),
extra_field=dict(),
in_files=dict(mandatory=True, ),
out_file=dict(usedefault=True, ),
out_file=dict(
extensions=None,
usedefault=True,
),
row_heading_title=dict(usedefault=True, ),
row_headings=dict(),
)
Expand All @@ -19,7 +22,7 @@ def test_MergeCSVFiles_inputs():
for metakey, value in list(metadata.items()):
assert getattr(inputs.traits()[key], metakey) == value
def test_MergeCSVFiles_outputs():
output_map = dict(csv_file=dict(), )
output_map = dict(csv_file=dict(extensions=None, ), )
outputs = MergeCSVFiles.output_spec()

for key, metadata in list(output_map.items()):
Expand Down
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