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Merge remote-tracking branch 'upstream/master' into patch-1
2 parents 73e98d2 + 3976524 commit 68b3003

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‎.travis.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
os: linux
2-
dist: xenial
2+
dist: bionic
33

44
language: python
55
# our build matrix

‎.zenodo.json

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -487,7 +487,7 @@
487487
"name": "Perkins, L. Nathan"
488488
},
489489
{
490-
"affiliation": "Otto-von-Guericke-University Magdeburg, Germany",
490+
"affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences",
491491
"name": "Contier, Oliver",
492492
"orcid": "0000-0002-2983-4709"
493493
},

‎nipype/algorithms/misc.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1408,7 +1408,7 @@ def merge_rois(in_files, in_idxs, in_ref, dtype=None, out_file=None):
14081408
# to avoid memory errors
14091409
if op.splitext(in_ref)[1] == ".gz":
14101410
try:
1411-
iflogger.info("uncompress %i", in_ref)
1411+
iflogger.info("uncompress %s", in_ref)
14121412
sp.check_call(["gunzip", in_ref], stdout=sp.PIPE, shell=True)
14131413
in_ref = op.splitext(in_ref)[0]
14141414
except:

‎nipype/algorithms/tests/test_auto_ACompCor.py

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

55
def test_ACompCor_inputs():
66
input_map = dict(
7-
components_file=dict(usedefault=True,),
8-
failure_mode=dict(usedefault=True,),
7+
components_file=dict(
8+
usedefault=True,
9+
),
10+
failure_mode=dict(
11+
usedefault=True,
12+
),
913
header_prefix=dict(),
10-
high_pass_cutoff=dict(usedefault=True,),
11-
ignore_initial_volumes=dict(usedefault=True,),
14+
high_pass_cutoff=dict(
15+
usedefault=True,
16+
),
17+
ignore_initial_volumes=dict(
18+
usedefault=True,
19+
),
1220
mask_files=dict(),
13-
mask_index=dict(requires=["mask_files"], xor=["merge_method"],),
21+
mask_index=dict(
22+
requires=["mask_files"],
23+
xor=["merge_method"],
24+
),
1425
mask_names=dict(),
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,),
26+
merge_method=dict(
27+
requires=["mask_files"],
28+
xor=["mask_index"],
29+
),
30+
num_components=dict(
31+
xor=["variance_threshold"],
32+
),
33+
pre_filter=dict(
34+
usedefault=True,
35+
),
36+
realigned_file=dict(
37+
extensions=None,
38+
mandatory=True,
39+
),
40+
regress_poly_degree=dict(
41+
usedefault=True,
42+
),
2043
repetition_time=dict(),
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"],),
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+
),
2557
)
2658
inputs = ACompCor.input_spec()
2759

@@ -32,9 +64,15 @@ def test_ACompCor_inputs():
3264

3365
def test_ACompCor_outputs():
3466
output_map = dict(
35-
components_file=dict(extensions=None,),
36-
metadata_file=dict(extensions=None,),
37-
pre_filter_file=dict(extensions=None,),
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+
),
3876
)
3977
outputs = ACompCor.output_spec()
4078

‎nipype/algorithms/tests/test_auto_ActivationCount.py

Lines changed: 17 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,14 @@
33

44

55
def test_ActivationCount_inputs():
6-
input_map = dict(in_files=dict(mandatory=True,), threshold=dict(mandatory=True,),)
6+
input_map = dict(
7+
in_files=dict(
8+
mandatory=True,
9+
),
10+
threshold=dict(
11+
mandatory=True,
12+
),
13+
)
714
inputs = ActivationCount.input_spec()
815

916
for key, metadata in list(input_map.items()):
@@ -13,9 +20,15 @@ def test_ActivationCount_inputs():
1320

1421
def test_ActivationCount_outputs():
1522
output_map = dict(
16-
acm_neg=dict(extensions=None,),
17-
acm_pos=dict(extensions=None,),
18-
out_file=dict(extensions=None,),
23+
acm_neg=dict(
24+
extensions=None,
25+
),
26+
acm_pos=dict(
27+
extensions=None,
28+
),
29+
out_file=dict(
30+
extensions=None,
31+
),
1932
)
2033
outputs = ActivationCount.output_spec()
2134

‎nipype/algorithms/tests/test_auto_AddCSVColumn.py

Lines changed: 13 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,14 @@ def test_AddCSVColumn_inputs():
66
input_map = dict(
77
extra_column_heading=dict(),
88
extra_field=dict(),
9-
in_file=dict(extensions=None, mandatory=True,),
10-
out_file=dict(extensions=None, usedefault=True,),
9+
in_file=dict(
10+
extensions=None,
11+
mandatory=True,
12+
),
13+
out_file=dict(
14+
extensions=None,
15+
usedefault=True,
16+
),
1117
)
1218
inputs = AddCSVColumn.input_spec()
1319

@@ -17,7 +23,11 @@ def test_AddCSVColumn_inputs():
1723

1824

1925
def test_AddCSVColumn_outputs():
20-
output_map = dict(csv_file=dict(extensions=None,),)
26+
output_map = dict(
27+
csv_file=dict(
28+
extensions=None,
29+
),
30+
)
2131
outputs = AddCSVColumn.output_spec()
2232

2333
for key, metadata in list(output_map.items()):

‎nipype/algorithms/tests/test_auto_AddCSVRow.py

Lines changed: 12 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,13 @@
44

55
def test_AddCSVRow_inputs():
66
input_map = dict(
7-
_outputs=dict(usedefault=True,), in_file=dict(extensions=None, mandatory=True,),
7+
_outputs=dict(
8+
usedefault=True,
9+
),
10+
in_file=dict(
11+
extensions=None,
12+
mandatory=True,
13+
),
814
)
915
inputs = AddCSVRow.input_spec()
1016

@@ -14,7 +20,11 @@ def test_AddCSVRow_inputs():
1420

1521

1622
def test_AddCSVRow_outputs():
17-
output_map = dict(csv_file=dict(extensions=None,),)
23+
output_map = dict(
24+
csv_file=dict(
25+
extensions=None,
26+
),
27+
)
1828
outputs = AddCSVRow.output_spec()
1929

2030
for key, metadata in list(output_map.items()):

‎nipype/algorithms/tests/test_auto_AddNoise.py

Lines changed: 26 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -4,12 +4,27 @@
44

55
def test_AddNoise_inputs():
66
input_map = dict(
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,),
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+
),
1328
)
1429
inputs = AddNoise.input_spec()
1530

@@ -19,7 +34,11 @@ def test_AddNoise_inputs():
1934

2035

2136
def test_AddNoise_outputs():
22-
output_map = dict(out_file=dict(extensions=None,),)
37+
output_map = dict(
38+
out_file=dict(
39+
extensions=None,
40+
),
41+
)
2342
outputs = AddNoise.output_spec()
2443

2544
for key, metadata in list(output_map.items()):

‎nipype/algorithms/tests/test_auto_ArtifactDetect.py

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

55
def test_ArtifactDetect_inputs():
66
input_map = dict(
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,),
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+
),
1119
mask_threshold=dict(),
12-
mask_type=dict(mandatory=True,),
20+
mask_type=dict(
21+
mandatory=True,
22+
),
1323
norm_threshold=dict(
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,),
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+
),
2662
)
2763
inputs = ArtifactDetect.input_spec()
2864

‎nipype/algorithms/tests/test_auto_CalculateMedian.py

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

55
def test_CalculateMedian_inputs():
66
input_map = dict(
7-
in_files=dict(), median_file=dict(), median_per_file=dict(usedefault=True,),
7+
in_files=dict(),
8+
median_file=dict(),
9+
median_per_file=dict(
10+
usedefault=True,
11+
),
812
)
913
inputs = CalculateMedian.input_spec()
1014

@@ -14,7 +18,9 @@ def test_CalculateMedian_inputs():
1418

1519

1620
def test_CalculateMedian_outputs():
17-
output_map = dict(median_files=dict(),)
21+
output_map = dict(
22+
median_files=dict(),
23+
)
1824
outputs = CalculateMedian.output_spec()
1925

2026
for key, metadata in list(output_map.items()):

‎nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py

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

55
def test_CalculateNormalizedMoments_inputs():
66
input_map = dict(
7-
moment=dict(mandatory=True,),
8-
timeseries_file=dict(extensions=None, mandatory=True,),
7+
moment=dict(
8+
mandatory=True,
9+
),
10+
timeseries_file=dict(
11+
extensions=None,
12+
mandatory=True,
13+
),
914
)
1015
inputs = CalculateNormalizedMoments.input_spec()
1116

@@ -15,7 +20,9 @@ def test_CalculateNormalizedMoments_inputs():
1520

1621

1722
def test_CalculateNormalizedMoments_outputs():
18-
output_map = dict(moments=dict(),)
23+
output_map = dict(
24+
moments=dict(),
25+
)
1926
outputs = CalculateNormalizedMoments.output_spec()
2027

2128
for key, metadata in list(output_map.items()):

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