Move (and simplify) the renaming of targets to `bids.increment_runind…

…ex()`

bidscoin/bids.py

@@ -2001,7 +2001,11 @@ def increment_runindex(outfolder: Path, bidsname: str, run: Run) -> str:
         # Rename run-less to run-1
         for runless_file in runless_files:
             LOGGER.verbose(f"Found run-2 files for <<>> index, renaming\n{runless_file} -> {run1_name}")
-            runless_file.replace((outfolder/run1_name).with_suffix(''.join(runless_file.suffixes)))
+            run1_file = (outfolder/run1_name).with_suffix(''.join(runless_file.suffixes))
+            runless_file.replace(run1_file)
+            if runless_file in targets:
+                targets.remove(runless_file)
+                targets.add(run1_file)
 
     return bidsname + bidsext
 

bidscoin/plugins/dcm2niix2bids.py

@@ -454,13 +454,6 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
                     LOGGER.warning(f"Overwriting existing {newbidsfile} file -- check your results carefully!")
                 dcm2niixfile.replace(newbidsfile)
                 targets.add(newbidsfile)
-                if bids.get_bidsvalue(newbidsfile, 'run') == '2' and str(run['bids'].get('run') or '') == "<<>>":
-                    # run-less file could be changed in the last call of increment_runindex within dcm2niixfiles loop
-                    runless_bidsfile = bids.insert_bidskeyval(newbidsfile, 'run', '', False)
-                    run1_bidsfile = bids.insert_bidskeyval(newbidsfile, 'run', '1', False)
-                    if runless_bidsfile in targets and not runless_bidsfile.is_file() and run1_bidsfile.is_file():
-                        targets.remove(runless_bidsfile)
-                        targets.add(run1_bidsfile)
 
                 # Rename all associated files (i.e. the json-, bval- and bvec-files)
                 for oldfile in outfolder.glob(dcm2niixfile.with_suffix('').stem + '.*'):