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Merge pull request #701 from effigies/fix/tests
FIX: Test failures
2 parents ecc1bc2 + b3bf23a commit ed97a42

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5 files changed

+31
-29
lines changed

5 files changed

+31
-29
lines changed

‎niworkflows/interfaces/bids.py

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -126,7 +126,7 @@ class BIDSInfo(SimpleInterface):
126126
127127
>>> bids_info = BIDSInfo(bids_dir=str(datadir / 'ds054'), bids_validate=False)
128128
>>> bids_info.inputs.in_file = '''\
129-
sub-01/func/ses-retest/sub-01_ses-retest_task-covertverbgeneration_rec-MB_acq-AP_run-1_bold.nii.gz'''
129+
sub-01/func/ses-retest/sub-01_ses-retest_task-covertverbgeneration_rec-MB_acq-AP_run-01_bold.nii.gz'''
130130
>>> res = bids_info.run()
131131
>>> res.outputs
132132
<BLANKLINE>
@@ -416,12 +416,12 @@ class DerivativesDataSink(SimpleInterface):
416416
>>> dsink.inputs.desc = 'preproc'
417417
>>> res = dsink.run()
418418
>>> res.outputs.out_file # doctest: +ELLIPSIS
419-
'.../niworkflows/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-1_\
419+
'.../niworkflows/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-01_\
420420
desc-preproc_bold.nii'
421421
422422
>>> bids_dir = tmpdir / 'bidsroot' / 'sub-02' / 'ses-noanat' / 'func'
423423
>>> bids_dir.mkdir(parents=True, exist_ok=True)
424-
>>> tricky_source = bids_dir / 'sub-02_ses-noanat_task-rest_run-1_bold.nii.gz'
424+
>>> tricky_source = bids_dir / 'sub-02_ses-noanat_task-rest_run-01_bold.nii.gz'
425425
>>> tricky_source.open('w').close()
426426
>>> dsink = DerivativesDataSink(base_directory=str(tmpdir), check_hdr=False)
427427
>>> dsink.inputs.in_file = str(tmpfile)
@@ -430,7 +430,7 @@ class DerivativesDataSink(SimpleInterface):
430430
>>> dsink.inputs.RepetitionTime = 0.75
431431
>>> res = dsink.run()
432432
>>> res.outputs.out_meta # doctest: +ELLIPSIS
433-
'.../niworkflows/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-1_\
433+
'.../niworkflows/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-01_\
434434
desc-preproc_bold.json'
435435
436436
>>> Path(res.outputs.out_meta).read_text().splitlines()[1]
@@ -450,7 +450,7 @@ class DerivativesDataSink(SimpleInterface):
450450
>>> dsink.inputs.RepetitionTime = 0.75
451451
>>> res = dsink.run()
452452
>>> res.outputs.out_meta # doctest: +ELLIPSIS
453-
'.../niworkflows/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-1_\
453+
'.../niworkflows/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-01_\
454454
space-MNI152NLin6Asym_res-01_desc-preproc_bold.json'
455455
456456
>>> lines = Path(res.outputs.out_meta).read_text().splitlines()
@@ -475,7 +475,7 @@ class DerivativesDataSink(SimpleInterface):
475475
>>> dsink.inputs.meta_dict = {'RepetitionTime': 1.75, 'SkullStripped': False, 'Z': 'val'}
476476
>>> res = dsink.run()
477477
>>> res.outputs.out_meta # doctest: +ELLIPSIS
478-
'.../niworkflows/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-1_\
478+
'.../niworkflows/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-01_\
479479
space-MNI152NLin6Asym_desc-preproc_bold.json'
480480
481481
>>> lines = Path(res.outputs.out_meta).read_text().splitlines()

‎niworkflows/interfaces/tests/test_bids.py

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -150,65 +150,65 @@
150150
BOLD_PATH,
151151
["aroma.csv"],
152152
{"suffix": "AROMAnoiseICs"},
153-
"sub-100185/func/sub-100185_task-machinegame_run-1_AROMAnoiseICs.csv",
153+
"sub-100185/func/sub-100185_task-machinegame_run-01_AROMAnoiseICs.csv",
154154
"da39a3ee5e6b4b0d3255bfef95601890afd80709",
155155
),
156156
(
157157
BOLD_PATH,
158158
["confounds.tsv"],
159159
{"suffix": "regressors", "desc": "confounds"},
160-
"sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.tsv",
160+
"sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_regressors.tsv",
161161
"da39a3ee5e6b4b0d3255bfef95601890afd80709",
162162
),
163163
(
164164
BOLD_PATH,
165165
["mixing.tsv"],
166166
{"suffix": "mixing", "desc": "MELODIC"},
167-
"sub-100185/func/sub-100185_task-machinegame_run-1_desc-MELODIC_mixing.tsv",
167+
"sub-100185/func/sub-100185_task-machinegame_run-01_desc-MELODIC_mixing.tsv",
168168
"da39a3ee5e6b4b0d3255bfef95601890afd80709",
169169
),
170170
(
171171
BOLD_PATH,
172172
["lh.func.gii"],
173173
{"space": "fsaverage", "density": "10k", "hemi": "L"},
174-
"sub-100185/func/sub-100185_task-machinegame_run-1_"
174+
"sub-100185/func/sub-100185_task-machinegame_run-01_"
175175
"hemi-L_space-fsaverage_den-10k_bold.func.gii",
176176
"da39a3ee5e6b4b0d3255bfef95601890afd80709",
177177
),
178178
(
179179
BOLD_PATH,
180180
["hcp.dtseries.nii"],
181181
{"space": "fsLR", "density": "91k"},
182-
"sub-100185/func/sub-100185_task-machinegame_run-1_"
182+
"sub-100185/func/sub-100185_task-machinegame_run-01_"
183183
"space-fsLR_den-91k_bold.dtseries.nii",
184184
"53d9b486d08fec5a952f68fcbcddb38a72818d4c",
185185
),
186186
(
187187
BOLD_PATH,
188188
["ref.nii"],
189189
{"space": "MNI", "suffix": "boldref"},
190-
"sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI_boldref.nii",
190+
"sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI_boldref.nii",
191191
"53d9b486d08fec5a952f68fcbcddb38a72818d4c",
192192
),
193193
(
194194
BOLD_PATH,
195195
["dseg.nii"],
196196
{"space": "MNI", "suffix": "dseg", "desc": "aseg"},
197-
"sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI_desc-aseg_dseg.nii",
197+
"sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI_desc-aseg_dseg.nii",
198198
"ddadc9be8224eebe0177a65bf87300f275e17e96",
199199
),
200200
(
201201
BOLD_PATH,
202202
["mask.nii"],
203203
{"space": "MNI", "suffix": "mask", "desc": "brain"},
204-
"sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI_desc-brain_mask.nii",
204+
"sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI_desc-brain_mask.nii",
205205
"f97a1877508139b42ea9fc476bdba367b001ab00",
206206
),
207207
(
208208
BOLD_PATH,
209209
["bold.nii"],
210210
{"space": "MNI", "desc": "preproc"},
211-
"sub-100185/func/sub-100185_task-machinegame_run-1_space-MNI_desc-preproc_bold.nii",
211+
"sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI_desc-preproc_bold.nii",
212212
"aa1eed935e6a8dcca646b0c78ee57218e30e2974",
213213
),
214214
# Nondeterministic order - do we really need this to work, or we can stay safe with
@@ -246,10 +246,10 @@
246246
"da39a3ee5e6b4b0d3255bfef95601890afd80709",
247247
),
248248
(
249-
"sub-07/ses-preop/anat/sub-07_ses-preop_run-1_T1w.nii.gz",
249+
"sub-07/ses-preop/anat/sub-07_ses-preop_run-01_T1w.nii.gz",
250250
["tfm.txt"],
251251
{"from": "orig", "to": "T1w", "suffix": "xfm"},
252-
"sub-07/ses-preop/anat/sub-07_ses-preop_run-1_from-orig_to-T1w_mode-image_xfm.txt",
252+
"sub-07/ses-preop/anat/sub-07_ses-preop_run-01_from-orig_to-T1w_mode-image_xfm.txt",
253253
"da39a3ee5e6b4b0d3255bfef95601890afd80709",
254254
),
255255
],
@@ -303,7 +303,7 @@ def test_DerivativesDataSink_build_path(
303303

304304
if dismiss_entities:
305305
if "run" in dismiss_entities:
306-
expectation = [e.replace("_run-1", "") for e in expectation]
306+
expectation = [e.replace("_run-01", "") for e in expectation]
307307

308308
if "session" in dismiss_entities:
309309
expectation = [
@@ -536,10 +536,10 @@ def test_DerivativesDataSink_fmapid(tmp_path):
536536
source_file = [
537537
(tmp_path / s)
538538
for s in [
539-
"sub-36/fmap/sub-36_dir-1_run-1_epi.nii.gz",
540-
"sub-36/fmap/sub-36_dir-1_run-2_epi.nii.gz",
541-
"sub-36/fmap/sub-36_dir-2_run-1_epi.nii.gz",
542-
"sub-36/fmap/sub-36_dir-2_run-2_epi.nii.gz",
539+
"sub-36/fmap/sub-36_dir-1_run-01_epi.nii.gz",
540+
"sub-36/fmap/sub-36_dir-1_run-02_epi.nii.gz",
541+
"sub-36/fmap/sub-36_dir-2_run-01_epi.nii.gz",
542+
"sub-36/fmap/sub-36_dir-2_run-02_epi.nii.gz",
543543
]
544544
]
545545
for fname in source_file:

‎niworkflows/tests/test_viz.py

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -140,7 +140,7 @@ def test_fmriplot(input_files):
140140
_cifti_timeseries(in_file)
141141
)
142142

143-
fMRIPlot(
143+
fig = fMRIPlot(
144144
timeseries,
145145
segments,
146146
tr=_get_tr(nb.load(in_file)),
@@ -151,10 +151,12 @@ def test_fmriplot(input_files):
151151
}),
152152
units={"FD": "mm"},
153153
paired_carpet=dtype == "cifti",
154-
).plot().savefig(
155-
os.path.join(save_artifacts, f"fmriplot_{dtype}{has_seg}.svg"),
156-
bbox_inches="tight",
157-
)
154+
).plot()
155+
if save_artifacts:
156+
fig.savefig(
157+
os.path.join(save_artifacts, f"fmriplot_{dtype}{has_seg}.svg"),
158+
bbox_inches="tight",
159+
)
158160

159161

160162
def test_plot_melodic_components(tmp_path):

‎niworkflows/utils/bids.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -222,7 +222,7 @@ def collect_data(
222222
layout.get(
223223
return_type="file",
224224
subject=participant_label,
225-
extension=["nii", "nii.gz"],
225+
extension=[".nii", ".nii.gz"],
226226
**query,
227227
)
228228
)

‎setup.cfg

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@ install_requires =
3636
numpy
3737
packaging
3838
pandas
39-
pybids >= 0.11.1
39+
pybids >= 0.15
4040
PyYAML
4141
scikit-image
4242
scipy

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