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Fabio Bernardoni
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run the make check-before-commit and edited the .zenodo file
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‎.zenodo.json

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Original file line numberDiff line numberDiff line change
@@ -313,6 +313,11 @@
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"name": "Geisler, Daniel",
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"orcid": "0000-0003-2076-5329"
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},
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{
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"affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universit\u00e4t Dresden, Dresden, Germany",
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"name": "Bernardoni, Fabio",
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"orcid": "0000-0002-5112-405X"
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},
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{
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"name": "Salvatore, John"
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},

‎Makefile

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@@ -2,7 +2,7 @@
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# Files are then pushed to sourceforge using rsync with a command like this:
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# rsync -e ssh nipype-0.1-py2.5.egg cburns,nipy@frs.sourceforge.net:/home/frs/project/n/ni/nipy/nipype/nipype-0.1/
44

5-
PYTHON ?= python
5+
PYTHON ?= python3
66

77
.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-coverage test html specs check-before-commit check gen-base-dockerfile gen-main-dockerfile gen-dockerfiles
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‎nipype/algorithms/tests/test_auto_ACompCor.py

Lines changed: 17 additions & 55 deletions
Original file line numberDiff line numberDiff line change
@@ -4,56 +4,24 @@
44

55
def test_ACompCor_inputs():
66
input_map = dict(
7-
components_file=dict(
8-
usedefault=True,
9-
),
10-
failure_mode=dict(
11-
usedefault=True,
12-
),
7+
components_file=dict(usedefault=True),
8+
failure_mode=dict(usedefault=True),
139
header_prefix=dict(),
14-
high_pass_cutoff=dict(
15-
usedefault=True,
16-
),
17-
ignore_initial_volumes=dict(
18-
usedefault=True,
19-
),
10+
high_pass_cutoff=dict(usedefault=True),
11+
ignore_initial_volumes=dict(usedefault=True),
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mask_files=dict(),
21-
mask_index=dict(
22-
requires=["mask_files"],
23-
xor=["merge_method"],
24-
),
13+
mask_index=dict(requires=["mask_files"], xor=["merge_method"]),
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mask_names=dict(),
26-
merge_method=dict(
27-
requires=["mask_files"],
28-
xor=["mask_index"],
29-
),
30-
num_components=dict(
31-
xor=["variance_threshold"],
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),
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pre_filter=dict(
34-
usedefault=True,
35-
),
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realigned_file=dict(
37-
extensions=None,
38-
mandatory=True,
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),
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regress_poly_degree=dict(
41-
usedefault=True,
42-
),
15+
merge_method=dict(requires=["mask_files"], xor=["mask_index"]),
16+
num_components=dict(xor=["variance_threshold"]),
17+
pre_filter=dict(usedefault=True),
18+
realigned_file=dict(extensions=None, mandatory=True),
19+
regress_poly_degree=dict(usedefault=True),
4320
repetition_time=dict(),
44-
save_metadata=dict(
45-
usedefault=True,
46-
),
47-
save_pre_filter=dict(
48-
usedefault=True,
49-
),
50-
use_regress_poly=dict(
51-
deprecated="0.15.0",
52-
new_name="pre_filter",
53-
),
54-
variance_threshold=dict(
55-
xor=["num_components"],
56-
),
21+
save_metadata=dict(usedefault=True),
22+
save_pre_filter=dict(usedefault=True),
23+
use_regress_poly=dict(deprecated="0.15.0", new_name="pre_filter"),
24+
variance_threshold=dict(xor=["num_components"]),
5725
)
5826
inputs = ACompCor.input_spec()
5927

@@ -64,15 +32,9 @@ def test_ACompCor_inputs():
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6533
def test_ACompCor_outputs():
6634
output_map = dict(
67-
components_file=dict(
68-
extensions=None,
69-
),
70-
metadata_file=dict(
71-
extensions=None,
72-
),
73-
pre_filter_file=dict(
74-
extensions=None,
75-
),
35+
components_file=dict(extensions=None),
36+
metadata_file=dict(extensions=None),
37+
pre_filter_file=dict(extensions=None),
7638
)
7739
outputs = ACompCor.output_spec()
7840

‎nipype/algorithms/tests/test_auto_ActivationCount.py

Lines changed: 4 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -3,14 +3,7 @@
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44

55
def test_ActivationCount_inputs():
6-
input_map = dict(
7-
in_files=dict(
8-
mandatory=True,
9-
),
10-
threshold=dict(
11-
mandatory=True,
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),
13-
)
6+
input_map = dict(in_files=dict(mandatory=True), threshold=dict(mandatory=True))
147
inputs = ActivationCount.input_spec()
158

169
for key, metadata in list(input_map.items()):
@@ -20,15 +13,9 @@ def test_ActivationCount_inputs():
2013

2114
def test_ActivationCount_outputs():
2215
output_map = dict(
23-
acm_neg=dict(
24-
extensions=None,
25-
),
26-
acm_pos=dict(
27-
extensions=None,
28-
),
29-
out_file=dict(
30-
extensions=None,
31-
),
16+
acm_neg=dict(extensions=None),
17+
acm_pos=dict(extensions=None),
18+
out_file=dict(extensions=None),
3219
)
3320
outputs = ActivationCount.output_spec()
3421

‎nipype/algorithms/tests/test_auto_AddCSVColumn.py

Lines changed: 3 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -6,14 +6,8 @@ def test_AddCSVColumn_inputs():
66
input_map = dict(
77
extra_column_heading=dict(),
88
extra_field=dict(),
9-
in_file=dict(
10-
extensions=None,
11-
mandatory=True,
12-
),
13-
out_file=dict(
14-
extensions=None,
15-
usedefault=True,
16-
),
9+
in_file=dict(extensions=None, mandatory=True),
10+
out_file=dict(extensions=None, usedefault=True),
1711
)
1812
inputs = AddCSVColumn.input_spec()
1913

@@ -23,11 +17,7 @@ def test_AddCSVColumn_inputs():
2317

2418

2519
def test_AddCSVColumn_outputs():
26-
output_map = dict(
27-
csv_file=dict(
28-
extensions=None,
29-
),
30-
)
20+
output_map = dict(csv_file=dict(extensions=None))
3121
outputs = AddCSVColumn.output_spec()
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3323
for key, metadata in list(output_map.items()):

‎nipype/algorithms/tests/test_auto_AddCSVRow.py

Lines changed: 2 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -4,13 +4,7 @@
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55
def test_AddCSVRow_inputs():
66
input_map = dict(
7-
_outputs=dict(
8-
usedefault=True,
9-
),
10-
in_file=dict(
11-
extensions=None,
12-
mandatory=True,
13-
),
7+
_outputs=dict(usedefault=True), in_file=dict(extensions=None, mandatory=True)
148
)
159
inputs = AddCSVRow.input_spec()
1610

@@ -20,11 +14,7 @@ def test_AddCSVRow_inputs():
2014

2115

2216
def test_AddCSVRow_outputs():
23-
output_map = dict(
24-
csv_file=dict(
25-
extensions=None,
26-
),
27-
)
17+
output_map = dict(csv_file=dict(extensions=None))
2818
outputs = AddCSVRow.output_spec()
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3020
for key, metadata in list(output_map.items()):

‎nipype/algorithms/tests/test_auto_AddNoise.py

Lines changed: 7 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -4,27 +4,12 @@
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55
def test_AddNoise_inputs():
66
input_map = dict(
7-
bg_dist=dict(
8-
mandatory=True,
9-
usedefault=True,
10-
),
11-
dist=dict(
12-
mandatory=True,
13-
usedefault=True,
14-
),
15-
in_file=dict(
16-
extensions=None,
17-
mandatory=True,
18-
),
19-
in_mask=dict(
20-
extensions=None,
21-
),
22-
out_file=dict(
23-
extensions=None,
24-
),
25-
snr=dict(
26-
usedefault=True,
27-
),
7+
bg_dist=dict(mandatory=True, usedefault=True),
8+
dist=dict(mandatory=True, usedefault=True),
9+
in_file=dict(extensions=None, mandatory=True),
10+
in_mask=dict(extensions=None),
11+
out_file=dict(extensions=None),
12+
snr=dict(usedefault=True),
2813
)
2914
inputs = AddNoise.input_spec()
3015

@@ -34,11 +19,7 @@ def test_AddNoise_inputs():
3419

3520

3621
def test_AddNoise_outputs():
37-
output_map = dict(
38-
out_file=dict(
39-
extensions=None,
40-
),
41-
)
22+
output_map = dict(out_file=dict(extensions=None))
4223
outputs = AddNoise.output_spec()
4324

4425
for key, metadata in list(output_map.items()):

‎nipype/algorithms/tests/test_auto_ArtifactDetect.py

Lines changed: 17 additions & 53 deletions
Original file line numberDiff line numberDiff line change
@@ -4,61 +4,25 @@
44

55
def test_ArtifactDetect_inputs():
66
input_map = dict(
7-
bound_by_brainmask=dict(
8-
usedefault=True,
9-
),
10-
global_threshold=dict(
11-
usedefault=True,
12-
),
13-
intersect_mask=dict(
14-
usedefault=True,
15-
),
16-
mask_file=dict(
17-
extensions=None,
18-
),
7+
bound_by_brainmask=dict(usedefault=True),
8+
global_threshold=dict(usedefault=True),
9+
intersect_mask=dict(usedefault=True),
10+
mask_file=dict(extensions=None),
1911
mask_threshold=dict(),
20-
mask_type=dict(
21-
mandatory=True,
22-
),
12+
mask_type=dict(mandatory=True),
2313
norm_threshold=dict(
24-
mandatory=True,
25-
xor=["rotation_threshold", "translation_threshold"],
26-
),
27-
parameter_source=dict(
28-
mandatory=True,
29-
),
30-
plot_type=dict(
31-
usedefault=True,
32-
),
33-
realigned_files=dict(
34-
mandatory=True,
35-
),
36-
realignment_parameters=dict(
37-
mandatory=True,
38-
),
39-
rotation_threshold=dict(
40-
mandatory=True,
41-
xor=["norm_threshold"],
42-
),
43-
save_plot=dict(
44-
usedefault=True,
45-
),
46-
translation_threshold=dict(
47-
mandatory=True,
48-
xor=["norm_threshold"],
49-
),
50-
use_differences=dict(
51-
maxlen=2,
52-
minlen=2,
53-
usedefault=True,
54-
),
55-
use_norm=dict(
56-
requires=["norm_threshold"],
57-
usedefault=True,
58-
),
59-
zintensity_threshold=dict(
60-
mandatory=True,
61-
),
14+
mandatory=True, xor=["rotation_threshold", "translation_threshold"]
15+
),
16+
parameter_source=dict(mandatory=True),
17+
plot_type=dict(usedefault=True),
18+
realigned_files=dict(mandatory=True),
19+
realignment_parameters=dict(mandatory=True),
20+
rotation_threshold=dict(mandatory=True, xor=["norm_threshold"]),
21+
save_plot=dict(usedefault=True),
22+
translation_threshold=dict(mandatory=True, xor=["norm_threshold"]),
23+
use_differences=dict(maxlen=2, minlen=2, usedefault=True),
24+
use_norm=dict(requires=["norm_threshold"], usedefault=True),
25+
zintensity_threshold=dict(mandatory=True),
6226
)
6327
inputs = ArtifactDetect.input_spec()
6428

‎nipype/algorithms/tests/test_auto_CalculateMedian.py

Lines changed: 2 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -4,11 +4,7 @@
44

55
def test_CalculateMedian_inputs():
66
input_map = dict(
7-
in_files=dict(),
8-
median_file=dict(),
9-
median_per_file=dict(
10-
usedefault=True,
11-
),
7+
in_files=dict(), median_file=dict(), median_per_file=dict(usedefault=True)
128
)
139
inputs = CalculateMedian.input_spec()
1410

@@ -18,9 +14,7 @@ def test_CalculateMedian_inputs():
1814

1915

2016
def test_CalculateMedian_outputs():
21-
output_map = dict(
22-
median_files=dict(),
23-
)
17+
output_map = dict(median_files=dict())
2418
outputs = CalculateMedian.output_spec()
2519

2620
for key, metadata in list(output_map.items()):

‎nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py

Lines changed: 3 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -4,13 +4,8 @@
44

55
def test_CalculateNormalizedMoments_inputs():
66
input_map = dict(
7-
moment=dict(
8-
mandatory=True,
9-
),
10-
timeseries_file=dict(
11-
extensions=None,
12-
mandatory=True,
13-
),
7+
moment=dict(mandatory=True),
8+
timeseries_file=dict(extensions=None, mandatory=True),
149
)
1510
inputs = CalculateNormalizedMoments.input_spec()
1611

@@ -20,9 +15,7 @@ def test_CalculateNormalizedMoments_inputs():
2015

2116

2217
def test_CalculateNormalizedMoments_outputs():
23-
output_map = dict(
24-
moments=dict(),
25-
)
18+
output_map = dict(moments=dict())
2619
outputs = CalculateNormalizedMoments.output_spec()
2720

2821
for key, metadata in list(output_map.items()):

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