[MAINT] Update code to pybids>=0.7 and niworkflows

Author: oesteban

fmriprep/__about__.py

@@ -84,17 +84,17 @@
 ]
 
 REQUIRES = [
-    'grabbit==0.2.3',
+    'grabbit==0.2.6',
     'indexed_gzip>=0.8.8',
     'nibabel>=2.2.1',
     'nilearn',
     'nipype>=1.1.6',
     'nitime',
-    'niworkflows>=0.6.1,<0.7.0a0',
+    'niworkflows>=0.6.1',
     'numpy',
     'pandas',
     'psutil>=5.4',
-    'pybids==0.6.5',
+    'pybids>=0.7.0,<8',
     'pyyaml',
     'scikit-image',
     'smriprep>=0.0.4,<0.1.0a0',
@@ -105,6 +105,8 @@
 
 
 LINKS_REQUIRES = [
+    'git+https://github.com/oesteban/niworkflows@'
+    'e3b6647c4dd9b29e459bd99e7a91548cf016ce3f#niworkflows-0.6.1',
 ]
 
 TESTS_REQUIRES = [

fmriprep/cli/run.py

@@ -607,7 +607,8 @@ def build_workflow(opts, retval):
     # First check that bids_dir looks like a BIDS folder
     bids_dir = os.path.abspath(opts.bids_dir)
     subject_list = collect_participants(
-        bids_dir, participant_label=opts.participant_label)
+        bids_dir, participant_label=opts.participant_label,
+        bids_validate=False)
 
     # Load base plugin_settings from file if --use-plugin
     if opts.use_plugin is not None:

fmriprep/workflows/base.py

@@ -379,7 +379,8 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
         }
         layout = None
     else:
-        subject_data, layout = collect_data(bids_dir, subject_id, task_id, echo_idx)
+        subject_data, layout = collect_data(
+            bids_dir, subject_id, task_id, echo_idx, bids_validate=False)
 
     # Make sure we always go through these two checks
     if not anat_only and subject_data['bold'] == []:
@@ -421,7 +422,9 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
     bidssrc = pe.Node(BIDSDataGrabber(subject_data=subject_data, anat_only=anat_only),
                       name='bidssrc')
 
-    bids_info = pe.Node(BIDSInfo(), name='bids_info', run_without_submitting=True)
+    bids_info = pe.Node(BIDSInfo(
+        bids_dir=bids_dir, bids_validate=False),
+        name='bids_info', run_without_submitting=True)
 
     summary = pe.Node(SubjectSummary(output_spaces=output_spaces, template=template),
                       name='summary', run_without_submitting=True)
@@ -464,12 +467,12 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
         (bidssrc, summary, [('t1w', 't1w'),
                             ('t2w', 't2w'),
                             ('bold', 'bold')]),
-        (bids_info, summary, [('subject_id', 'subject_id')]),
+        (bids_info, summary, [('subject', 'subject_id')]),
+        (bids_info, anat_preproc_wf, [(('subject', _prefix), 'inputnode.subject_id')]),
         (bidssrc, anat_preproc_wf, [('t1w', 'inputnode.t1w'),
                                     ('t2w', 'inputnode.t2w'),
                                     ('roi', 'inputnode.roi'),
                                     ('flair', 'inputnode.flair')]),
-        (summary, anat_preproc_wf, [('subject_id', 'inputnode.subject_id')]),
         (bidssrc, ds_report_summary, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
         (summary, ds_report_summary, [('out_report', 'in_file')]),
         (bidssrc, ds_report_about, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),
@@ -532,3 +535,10 @@ def init_single_subject_wf(subject_id, task_id, echo_idx, name, reportlets_dir,
         ])
 
     return workflow
+
+
+def _prefix(subid):
+    if subid.startswith('sub-'):
+        return subid
+    return '-'.join(('sub', subid))
+

fmriprep/workflows/bold/base.py

@@ -264,8 +264,8 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
     else:
         # Find associated sbref, if possible
         entities = layout.parse_file_entities(ref_file)
-        entities['type'] = 'sbref'
-        files = layout.get(**entities, extensions=['nii', 'nii.gz'])
+        entities['suffix'] = 'sbref'
+        files = layout.get(extensions=['nii', 'nii.gz'], **entities)
         refbase = os.path.basename(ref_file)
         if 'sbref' in ignore:
             LOGGER.info("Single-band reference files ignored.")

fmriprep/workflows/fieldmap/phdiff.py

@@ -73,7 +73,8 @@ def _pick1st(inlist):
         return inlist[0]
 
     # Read phasediff echo times
-    meta = pe.Node(ReadSidecarJSON(), name='meta', mem_gb=0.01, run_without_submitting=True)
+    meta = pe.Node(ReadSidecarJSON(bids_validate=False),
+        name='meta', mem_gb=0.01, run_without_submitting=True)
 
     # Merge input magnitude images
     magmrg = pe.Node(IntraModalMerge(), name='magmrg')

requirements.txt

@@ -1,5 +1,5 @@
-grabbit==0.2.3
-pybids==0.6.5
-niworkflows>=0.6.1,<0.7.0a0
+grabbit==0.2.6
+pybids>=0.7.0,<0.8
+git+https://github.com/oesteban/niworkflows@e3b6647c4dd9b29e459bd99e7a91548cf016ce3f#niworkflows-0.6.1
 smriprep>=0.0.4,<0.1.0a0
 templateflow>=0.0.4