Merge tag '23.1.2'

23.1.2 (June 16, 2023)

Bug fix release in the 23.1.x series.

This release correctly generates ``*_space-fsLR_desc-reg_sphere.surf.gii``,
which was previously a copy of the standard ``*_desc-reg_sphere.surf.gii``.
Additionally, warnings are now correctly emitted when AROMA-related CLI
options are used.

* CI: Clean up pre-release builds (#3040)

Author: effigies

CHANGES.rst

@@ -1,3 +1,16 @@
+23.1.2 (June 16, 2023)
+======================
+
+Bug fix release in the 23.1.x series.
+
+This release correctly generates ``*_space-fsLR_desc-reg_sphere.surf.gii``,
+which was previously a copy of the standard ``*_desc-reg_sphere.surf.gii``.
+Additionally, warnings are now correctly emitted when AROMA-related CLI
+options are used.
+
+* CI: Clean up pre-release builds (#3040)
+
+
 23.1.1 (June 14, 2023)
 ======================
 

fmriprep/cli/run.py

@@ -50,7 +50,7 @@ def main():
             config.workflow.aroma_melodic_dim,
         )
     ):
-        warnings.warn(
+        config.loggers.cli.warning(
             "ICA-AROMA was removed in fMRIPrep 23.1.0. The --use-aroma, --aroma-err-on-warn, "
             "and --aroma-melodic-dim flags will error in fMRIPrep 24.0.0."
         )

fmriprep/config.py

@@ -604,9 +604,10 @@ def init(cls):
         """
         from nipype import config as ncfg
 
-        _handler = logging.StreamHandler(stream=sys.stdout)
-        _handler.setFormatter(logging.Formatter(fmt=cls._fmt, datefmt=cls._datefmt))
-        cls.cli.addHandler(_handler)
+        if not cls.cli.hasHandlers():
+            _handler = logging.StreamHandler(stream=sys.stdout)
+            _handler.setFormatter(logging.Formatter(fmt=cls._fmt, datefmt=cls._datefmt))
+            cls.cli.addHandler(_handler)
         cls.default.setLevel(execution.log_level)
         cls.cli.setLevel(execution.log_level)
         cls.interface.setLevel(execution.log_level)

requirements.txt

@@ -294,7 +294,7 @@ six==1.16.0
     #   apscheduler
     #   isodate
     #   python-dateutil
-smriprep==0.12.0
+smriprep==0.12.1
     # via fmriprep (pyproject.toml)
 sqlalchemy==2.0.15
     # via pybids