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-47
lines changed

4 files changed

+33
-47
lines changed

‎.github/workflows/test.yml

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ jobs:
3131
matrix:
3232
py: ['3.13', '3.12', '3.11', '3.10', '3.9']
3333
os: [ubuntu-latest]
34-
env: ["test", "dev"]
34+
env: [test, dev]
3535
steps:
3636
- uses: actions/checkout@v4
3737
- name: Install the latest version of uv
@@ -47,5 +47,3 @@ jobs:
4747
- name: Run test suite
4848
run: |
4949
tox run --list-dependencies -e ${{ matrix.env }}
50-
51-

‎notebooks/nilearn_notebooks_dev.py

Lines changed: 14 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ def _(mo):
1919
r"""
2020
# Using nilearn in a marimo notebook
2121
22-
This notebook is mostly for nilearn developpers
22+
This notebook is mostly for nilearn developers
2323
to make sure nilearn functionalities run well
2424
in a marimo notebook.
2525
@@ -110,6 +110,7 @@ def _(mo):
110110
@app.cell
111111
def _(motor_activation_image):
112112
from nilearn.plotting import view_img
113+
113114
html_fig = view_img(motor_activation_image)
114115
html_fig
115116
return html_fig, view_img
@@ -123,11 +124,10 @@ def _(mo):
123124

124125
@app.cell
125126
def _(mo, motor_activation_image, show):
126-
from nilearn.datasets import load_fsaverage
127-
from nilearn.surface import SurfaceImage
128127
import numpy as np
128+
from nilearn.datasets import load_fsaverage, load_fsaverage_data
129129
from nilearn.plotting import plot_surf_stat_map
130-
from nilearn.datasets import load_fsaverage_data
130+
from nilearn.surface import SurfaceImage
131131

132132
fsaverage_meshes = load_fsaverage()
133133

@@ -203,8 +203,8 @@ def _(mo):
203203

204204
@app.cell
205205
def _(motor_activation_image):
206-
from nilearn.maskers import NiftiMasker
207206
from nilearn.datasets import fetch_development_fmri
207+
from nilearn.maskers import NiftiMasker
208208

209209
nifti_masker = NiftiMasker(
210210
standardize="zscore_sample",
@@ -229,8 +229,8 @@ def _(mo):
229229

230230
@app.cell
231231
def _(motor_activation_image):
232-
from nilearn.maskers import NiftiLabelsMasker
233232
from nilearn.datasets import fetch_atlas_schaefer_2018
233+
from nilearn.maskers import NiftiLabelsMasker
234234

235235
atlas_schaefer_2018 = fetch_atlas_schaefer_2018()
236236

@@ -302,9 +302,7 @@ def _(SurfaceImage, fsaverage_meshes, motor_activation_surface_image):
302302

303303
atlas_msdl = fetch_atlas_msdl()
304304

305-
surf_atlas = SurfaceImage.from_volume(
306-
volume_img=atlas_msdl.maps, mesh=fsaverage_meshes["pial"]
307-
)
305+
surf_atlas = SurfaceImage.from_volume(volume_img=atlas_msdl.maps, mesh=fsaverage_meshes["pial"])
308306

309307
surface_map_masker = SurfaceMapsMasker(surf_atlas).fit()
310308
surface_map_masker.transform(motor_activation_surface_image)
@@ -353,7 +351,7 @@ def _(mo):
353351

354352
@app.cell
355353
def _():
356-
from nilearn.datasets import fetch_ds000030_urls, select_from_index, fetch_openneuro_dataset
354+
from nilearn.datasets import fetch_ds000030_urls, fetch_openneuro_dataset, select_from_index
357355

358356
def fetch_bids_data():
359357
_, urls = fetch_ds000030_urls()
@@ -373,13 +371,12 @@ def fetch_bids_data():
373371
"*task-scap*",
374372
"*task-task*",
375373
]
376-
urls = select_from_index(
377-
urls, exclusion_filters=exclusion_patterns, n_subjects=1
378-
)
374+
urls = select_from_index(urls, exclusion_filters=exclusion_patterns, n_subjects=1)
379375

380376
data_dir, _ = fetch_openneuro_dataset(urls=urls)
381377

382378
return data_dir
379+
383380
return (
384381
fetch_bids_data,
385382
fetch_ds000030_urls,
@@ -411,7 +408,7 @@ def _(fetch_bids_data):
411408
space_label,
412409
smoothing_fwhm=5.0,
413410
derivatives_folder=derivatives_folder,
414-
slice_time_ref=0.0
411+
slice_time_ref=0.0,
415412
)
416413

417414
flm = models[0]
@@ -426,12 +423,8 @@ def _(fetch_bids_data):
426423
/ "stopsignal.feat"
427424
/ "design.mat"
428425
)
429-
design_matrices = get_design_from_fslmat(
430-
fsl_design_matrix_path, column_names=None
431-
)
432-
design_columns = [
433-
f"cond_{int(i):02}" for i in range(len(design_matrices.columns))
434-
]
426+
design_matrices = get_design_from_fslmat(fsl_design_matrix_path, column_names=None)
427+
design_columns = [f"cond_{int(i):02}" for i in range(len(design_matrices.columns))]
435428
design_columns[0] = "Go"
436429
design_columns[4] = "StopSuccess"
437430
design_matrices.columns = design_columns
@@ -479,6 +472,7 @@ def _(flm_report):
479472
@app.cell
480473
def _():
481474
import marimo as mo
475+
482476
return (mo,)
483477

484478

‎notebooks/nilearn_notebooks_stable.py

Lines changed: 17 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ def _(mo):
1919
r"""
2020
# Using nilearn in a marimo notebook
2121
22-
This notebook is mostly for nilearn developpers
22+
This notebook is mostly for nilearn developers
2323
to make sure nilearn functionalities run well
2424
in a marimo notebook.
2525
@@ -96,6 +96,7 @@ def _(mo):
9696
@app.cell
9797
def _(motor_activation_image):
9898
from nilearn.plotting import view_img
99+
99100
html_fig = view_img(motor_activation_image)
100101
html_fig
101102
return html_fig, view_img
@@ -109,11 +110,10 @@ def _(mo):
109110

110111
@app.cell
111112
def _(mo, motor_activation_image, show):
112-
from nilearn.datasets import load_fsaverage
113-
from nilearn.surface import SurfaceImage
114113
import numpy as np
114+
from nilearn.datasets import load_fsaverage, load_fsaverage_data
115115
from nilearn.plotting import plot_surf_stat_map
116-
from nilearn.datasets import load_fsaverage_data
116+
from nilearn.surface import SurfaceImage
117117

118118
fsaverage_meshes = load_fsaverage()
119119

@@ -189,8 +189,8 @@ def _(mo):
189189

190190
@app.cell
191191
def _(motor_activation_image):
192-
from nilearn.maskers import NiftiMasker
193192
from nilearn.datasets import fetch_development_fmri
193+
from nilearn.maskers import NiftiMasker
194194

195195
nifti_masker = NiftiMasker(
196196
standardize="zscore_sample",
@@ -215,8 +215,8 @@ def _(mo):
215215

216216
@app.cell
217217
def _(motor_activation_image):
218-
from nilearn.maskers import NiftiLabelsMasker
219218
from nilearn.datasets import fetch_atlas_schaefer_2018
219+
from nilearn.maskers import NiftiLabelsMasker
220220

221221
atlas_schaefer_2018 = fetch_atlas_schaefer_2018()
222222

@@ -288,9 +288,7 @@ def _(SurfaceImage, fsaverage_meshes, motor_activation_surface_image):
288288

289289
atlas_msdl = fetch_atlas_msdl()
290290

291-
surf_atlas = SurfaceImage.from_volume(
292-
volume_img=atlas_msdl.maps, mesh=fsaverage_meshes["pial"]
293-
)
291+
surf_atlas = SurfaceImage.from_volume(volume_img=atlas_msdl.maps, mesh=fsaverage_meshes["pial"])
294292

295293
surface_map_masker = SurfaceMapsMasker(surf_atlas).fit()
296294
surface_map_masker.transform(motor_activation_surface_image)
@@ -339,11 +337,11 @@ def _(mo):
339337

340338
@app.cell
341339
def _():
342-
from nilearn.datasets import fetch_ds000030_urls, select_from_index, fetch_openneuro_dataset
340+
from nilearn.datasets import fetch_ds000030_urls, fetch_openneuro_dataset, select_from_index
343341

344342
def fetch_bids_data():
345343
_, urls = fetch_ds000030_urls()
346-
344+
347345
exclusion_patterns = [
348346
"*group*",
349347
"*phenotype*",
@@ -359,13 +357,12 @@ def fetch_bids_data():
359357
"*task-scap*",
360358
"*task-task*",
361359
]
362-
urls = select_from_index(
363-
urls, exclusion_filters=exclusion_patterns, n_subjects=1
364-
)
365-
360+
urls = select_from_index(urls, exclusion_filters=exclusion_patterns, n_subjects=1)
361+
366362
data_dir, _ = fetch_openneuro_dataset(urls=urls)
367-
363+
368364
return data_dir
365+
369366
return (
370367
fetch_bids_data,
371368
fetch_ds000030_urls,
@@ -397,7 +394,7 @@ def _(fetch_bids_data):
397394
space_label,
398395
smoothing_fwhm=5.0,
399396
derivatives_folder=derivatives_folder,
400-
slice_time_ref=0.0
397+
slice_time_ref=0.0,
401398
)
402399

403400
flm = models[0]
@@ -412,12 +409,8 @@ def _(fetch_bids_data):
412409
/ "stopsignal.feat"
413410
/ "design.mat"
414411
)
415-
design_matrices = get_design_from_fslmat(
416-
fsl_design_matrix_path, column_names=None
417-
)
418-
design_columns = [
419-
f"cond_{int(i):02}" for i in range(len(design_matrices.columns))
420-
]
412+
design_matrices = get_design_from_fslmat(fsl_design_matrix_path, column_names=None)
413+
design_columns = [f"cond_{int(i):02}" for i in range(len(design_matrices.columns))]
421414
design_columns[0] = "Go"
422415
design_columns[4] = "StopSuccess"
423416
design_matrices.columns = design_columns
@@ -465,6 +458,7 @@ def _(flm_report):
465458
@app.cell
466459
def _():
467460
import marimo as mo
461+
468462
return (mo,)
469463

470464

‎pyproject.toml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -84,7 +84,7 @@ unfixable = []
8484
max-complexity = 15
8585

8686
[tool.ruff.lint.per-file-ignores]
87-
"notebooks/**/*.py" = ["E501", "E741"]
87+
"notebooks/**/*.py" = ["D100", "E501", "E741"]
8888
"scripts/build.py" = ["E501", "PTH118", "PTH103", "PTH123", "PTH120"]
8989

9090
[tool.ruff.lint.pydocstyle]

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