Merge pull request #326 from effigies/fix/misc

FIX: Minor fixes

fitlins/cli/run.py

@@ -100,7 +100,7 @@ def get_parser():
                         help='regex pattern or string to ignore files')
     g_bids.add_argument('--desc-label', action='store', default='preproc',
                         help="use BOLD files with the provided description label")
-    g_bids.add_argument('--database-path', action='store', default=None,
+    g_bids.add_argument('--database-path', action='store', default=None, type=op.abspath,
                         help="Path to directory containing SQLite database indices "
                              "for this BIDS dataset. "
                              "If a value is passed and the file already exists, "

fitlins/utils/bids.py

@@ -71,7 +71,7 @@ def collect_participants(layout, participant_label=None, strict=False):
 
 
     """
-    all_participants = layout.get_subjects()
+    all_participants = sorted(layout.get_subjects())
 
     # Error: bids_dir does not contain subjects
     if not all_participants:
@@ -87,9 +87,10 @@ def collect_participants(layout, participant_label=None, strict=False):
         return all_participants
 
     # Drop sub- prefixes
-    participant_label = [sub[4:] if sub.startswith('sub-') else sub for sub in participant_label]
+    participant_label = [sub[4:] if sub.startswith('sub-') else sub
+                         for sub in participant_label]
 
-    found_label = layout.get_subjects(subject=participant_label)
+    found_label = sorted(layout.get_subjects(subject=participant_label))
 
     if not found_label:
         raise BIDSError('Could not find participants [{}]'.format(

fitlins/viz/reports.py

@@ -130,4 +130,5 @@ def write_full_report(report_dict, run_context, deriv_dir):
         deriv_dir, fl_layout.build_path(
             {'model': model}, PATH_PATTERNS, validate=False))
     html = tpl.render(deroot({**report_dict, **run_context}, op.dirname(target_file)))
+    Path(target_file).parent.mkdir(parents=True, exist_ok=True)
     Path(target_file).write_text(html)