Merge pull request #1707 from oesteban/maint/pybids-0.9.x-extensions

MAINT: Remove old ``extensions`` entity selector for pybids queries

fmriprep/cli/run.py

@@ -399,7 +399,7 @@ def main():
         if opts.run_reconall:
             from templateflow import api
             from niworkflows.utils.misc import _copy_any
-            dseg_tsv = str(api.get('fsaverage', suffix='dseg', extensions=['.tsv']))
+            dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
             _copy_any(dseg_tsv,
                       str(output_dir / 'fmriprep' / 'desc-aseg_dseg.tsv'))
             _copy_any(dseg_tsv,

fmriprep/workflows/bold/base.py

@@ -314,7 +314,8 @@ def init_func_preproc_wf(
         # Find associated sbref, if possible
         entities = layout.parse_file_entities(ref_file)
         entities['suffix'] = 'sbref'
-        files = layout.get(return_type='file', extensions=['nii', 'nii.gz'], **entities)
+        entities['extension'] = ['nii', 'nii.gz']  # Overwrite extensions
+        files = layout.get(return_type='file', **entities)
         refbase = os.path.basename(ref_file)
         if 'sbref' in ignore:
             LOGGER.info("Single-band reference files ignored.")

fmriprep/workflows/bold/confounds.py

@@ -482,7 +482,7 @@ def init_carpetplot_wf(standard_spaces, mem_gb, metadata, name="bold_carpet_wf")
         float=True,
         input_image=str(get_template(
             'MNI152NLin2009cAsym', resolution=1, desc='carpet',
-            suffix='dseg', extensions=['.nii', '.nii.gz'])),
+            suffix='dseg', extension=['.nii', '.nii.gz'])),
         dimension=3, default_value=0, interpolation='MultiLabel'),
         name='resample_parc')
 

setup.cfg

@@ -20,9 +20,9 @@ classifiers =
 [options]
 python_requires = >=3.5
 install_requires =
-    niworkflows ~= 0.10.0
-    smriprep ~= 0.3.0
-    templateflow ~= 0.4.1rc1
+    niworkflows ~= 0.10.1
+    smriprep ~= 0.3.1
+    templateflow ~= 0.4.1
     nibabel >=2.2.1
     indexed_gzip >=0.8.8
     nilearn !=0.5.0, !=0.5.1