(maint) reconcile with upstream

Author: rciric

.circleci/ds005_partial_outputs.txt

@@ -43,6 +43,7 @@ fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.nii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L.func.gii

fmriprep/workflows/bold/base.py

@@ -64,35 +64,37 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         from fmriprep.workflows.bold import init_func_preproc_wf
         from collections import namedtuple
         BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
-        wf = init_func_preproc_wf('/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
-                                  omp_nthreads=1,
-                                  ignore=[],
-                                  freesurfer=True,
-                                  reportlets_dir='.',
-                                  output_dir='.',
-                                  template='MNI152NLin2009cAsym',
-                                  output_spaces=['T1w', 'fsnative',
-                                                 'template', 'fsaverage5'],
-                                  debug=False,
-                                  use_bbr=True,
-                                  t2s_coreg=False,
-                                  bold2t1w_dof=9,
-                                  fmap_bspline=True,
-                                  fmap_demean=True,
-                                  use_syn=True,
-                                  force_syn=True,
-                                  low_mem=False,
-                                  template_out_grid='native',
-                                  medial_surface_nan=False,
-                                  cifti_output=False,
-                                  use_aroma=False,
-                                  err_on_aroma_warn=False,
-                                  aroma_melodic_dim=-200,
-                                  return_all_components=False,
-                                  fd_spike_thr=0.5,
-                                  dv_spike_thr=1.5,
-                                  num_bold=1,
-                                  layout=BIDSLayout()))
+        wf = init_func_preproc_wf(
+            '/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
+            omp_nthreads=1,
+            ignore=[],
+            freesurfer=True,
+            reportlets_dir='.',
+            output_dir='.',
+            template='MNI152NLin2009cAsym',
+            output_spaces=['T1w', 'fsnative',
+            'template', 'fsaverage5'],
+            debug=False,
+            use_bbr=True,
+            t2s_coreg=False,
+            bold2t1w_dof=9,
+            fmap_bspline=True,
+            fmap_demean=True,
+            use_syn=True,
+            force_syn=True,
+            low_mem=False,
+            template_out_grid='native',
+            medial_surface_nan=False,
+            cifti_output=False,
+            use_aroma=False,
+            err_on_aroma_warn=False,
+            aroma_melodic_dim=-200,
+            return_all_components=False,
+            fd_spike_thr=0.5,
+            dv_spike_thr=1.5,
+            num_bold=1,
+            layout=BIDSLayout(),
+        )
 
     **Parameters**