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

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merged 1 commit into from
Mar 24, 2025
Merged

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

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44 changes: 0 additions & 44 deletions fmriprep/cli/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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'),
Expand Down Expand Up @@ -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'],
Expand Down Expand Up @@ -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',
Expand Down
13 changes: 0 additions & 13 deletions fmriprep/cli/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
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