feat(cli): Remove CLI flags with expired deprecation periods (#3445)

Pretty straightforward. We said we'd remove these things, and now
they're removed. It's been a full year and two minor versions with the
deprecation warnings.

Author: effigies

fmriprep/cli/parser.py

@@ -43,11 +43,6 @@ def _build_parser(**kwargs):
 
     deprecations = {
         # parser attribute name: (replacement flag, version slated to be removed in)
-        'use_aroma': (None, '24.0.0'),
-        'aroma_melodic_dim': (None, '24.0.0'),
-        'aroma_err_on_warn': (None, '24.0.0'),
-        'bold2t1w_init': ('--bold2anat-init', '24.2.0'),
-        'bold2t1w_dof': ('--bold2anat-dof', '24.2.0'),
         'force_bbr': ('--force bbr', '26.0.0'),
         'force_no_bbr': ('--force no-bbr', '26.0.0'),
         'force_syn': ('--force syn-sdc', '26.0.0'),
@@ -376,19 +371,6 @@ def _slice_time_ref(value, parser):
         action='store_true',
         help='Treat dataset as longitudinal - may increase runtime',
     )
-    g_conf.add_argument(
-        '--bold2t1w-init',
-        action=DeprecatedAction,
-        choices=['register', 'header'],
-        help='Deprecated - use `--bold2anat-init` instead.',
-    )
-    g_conf.add_argument(
-        '--bold2t1w-dof',
-        action=DeprecatedAction,
-        choices=[6, 9, 12],
-        type=int,
-        help='Deprecated - use `--bold2anat-dof` instead.',
-    )
     g_conf.add_argument(
         '--bold2anat-init',
         choices=['auto', 't1w', 't2w', 'header'],
@@ -525,32 +507,6 @@ def _slice_time_ref(value, parser):
         help='Disable Multimodal Surface Matching surface registration.',
     )
 
-    g_aroma = parser.add_argument_group(
-        '[DEPRECATED] Options for running ICA_AROMA',
-        description=(
-            'If you would like to apply ICA-AROMA to fMRIPrep derivatives, '
-            'please consider using fMRIPost-AROMA (https://fmripost-aroma.readthedocs.io/)'
-        ),
-    )
-    g_aroma.add_argument(
-        '--use-aroma',
-        action=DeprecatedAction,
-        help='Deprecated. Will raise an error in 24.0.',
-    )
-    g_aroma.add_argument(
-        '--aroma-melodic-dimensionality',
-        dest='aroma_melodic_dim',
-        action=DeprecatedAction,
-        type=int,
-        help='Deprecated. Will raise an error in 24.0.',
-    )
-    g_aroma.add_argument(
-        '--error-on-aroma-warnings',
-        action=DeprecatedAction,
-        dest='aroma_err_on_warn',
-        help='Deprecated. Will raise an error in 24.0.',
-    )
-
     g_confounds = parser.add_argument_group('Options relating to confounds')
     g_confounds.add_argument(
         '--return-all-components',

fmriprep/cli/run.py

@@ -39,19 +39,6 @@ def main():
 
     parse_args()
 
-    # Deprecated flags
-    if any(
-        (
-            config.workflow.use_aroma,
-            config.workflow.aroma_err_on_warn,
-            config.workflow.aroma_melodic_dim,
-        )
-    ):
-        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.'
-        )
-
     # Code Carbon
     if config.execution.track_carbon:
         from codecarbon import OfflineEmissionsTracker