Drop fmripost_aroma_dir in favor of output_dir.

src/fmripost_aroma/cli/parser.py

@@ -543,9 +543,6 @@ def parse_args(args=None, namespace=None):
     work_dir = config.execution.work_dir
     version = config.environment.version
 
-    if config.execution.fmripost_aroma_dir is None:
-        config.execution.fmripost_aroma_dir = output_dir
-
     # Wipe out existing work_dir
     if opts.clean_workdir and work_dir.exists():
         from niworkflows.utils.misc import clean_directory
@@ -585,7 +582,7 @@ def parse_args(args=None, namespace=None):
         validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
 
     # Setup directories
-    config.execution.log_dir = config.execution.fmripost_aroma_dir / 'logs'
+    config.execution.log_dir = config.execution.output_dir / 'logs'
     # Check and create output and working directories
     config.execution.log_dir.mkdir(exist_ok=True, parents=True)
     work_dir.mkdir(exist_ok=True, parents=True)

src/fmripost_aroma/cli/run.py

@@ -152,7 +152,7 @@ def main():
             from fmripost_aroma.utils.telemetry import process_crashfile
 
             crashfolders = [
-                config.execution.fmripost_aroma_dir
+                config.execution.output_dir
                 / f'sub-{s}'
                 / 'log'
                 / config.execution.run_uuid
@@ -176,7 +176,7 @@ def main():
             sentry_sdk.capture_message(success_message, level='info')
 
         # Bother users with the boilerplate only iff the workflow went okay.
-        boiler_file = config.execution.fmripost_aroma_dir / 'logs' / 'CITATION.md'
+        boiler_file = config.execution.output_dir / 'logs' / 'CITATION.md'
         if boiler_file.exists():
             if config.environment.exec_env in (
                 'singularity',
@@ -198,9 +198,9 @@ def main():
             from templateflow import api
 
             dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
-            _copy_any(dseg_tsv, str(config.execution.fmripost_aroma_dir / 'desc-aseg_dseg.tsv'))
+            _copy_any(dseg_tsv, str(config.execution.output_dir / 'desc-aseg_dseg.tsv'))
             _copy_any(
-                dseg_tsv, str(config.execution.fmripost_aroma_dir / 'desc-aparcaseg_dseg.tsv')
+                dseg_tsv, str(config.execution.output_dir / 'desc-aparcaseg_dseg.tsv')
             )
         errno = 0
     finally:
@@ -216,13 +216,13 @@ def main():
         # Generate reports phase
         failed_reports = generate_reports(
             subject_list=config.execution.participant_label,
-            output_dir=config.execution.fmripost_aroma_dir,
+            output_dir=config.execution.output_dir,
             run_uuid=config.execution.run_uuid,
         )
         write_derivative_description(
-            config.execution.bids_dir, config.execution.fmripost_aroma_dir
+            config.execution.bids_dir, config.execution.output_dir
         )
-        write_bidsignore(config.execution.fmripost_aroma_dir)
+        write_bidsignore(config.execution.output_dir)
 
         if sentry_sdk is not None and failed_reports:
             sentry_sdk.capture_message(

src/fmripost_aroma/cli/workflow.py

@@ -48,7 +48,7 @@ def build_workflow(config_file, retval):
     config.load(config_file)
     build_log = config.loggers.workflow
 
-    fmripost_aroma_dir = config.execution.fmripost_aroma_dir
+    output_dir = config.execution.output_dir
     version = config.environment.version
 
     retval['return_code'] = 1
@@ -68,7 +68,7 @@ def build_workflow(config_file, retval):
     msg = check_pipeline_version(
         'fMRIPost-AROMA',
         version,
-        fmripost_aroma_dir / 'dataset_description.json',
+        output_dir / 'dataset_description.json',
     )
     if msg is not None:
         build_log.warning(msg)
@@ -92,7 +92,7 @@ def build_workflow(config_file, retval):
         build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
         retval['return_code'] = generate_reports(
             subject_list=config.execution.participant_label,
-            output_dir=config.execution.fmripost_aroma_dir,
+            output_dir=config.execution.output_dir,
             run_uuid=config.execution.run_uuid,
         )
         return retval
@@ -137,7 +137,7 @@ def build_boilerplate(config_file, workflow):
     from fmripost_aroma import config
 
     config.load(config_file)
-    logs_path = config.execution.fmripost_aroma_dir / 'logs'
+    logs_path = config.execution.output_dir / 'logs'
     boilerplate = workflow.visit_desc()
     citation_files = {ext: logs_path / f'CITATION.{ext}' for ext in ('bib', 'tex', 'md', 'html')}
 

src/fmripost_aroma/config.py

@@ -403,8 +403,6 @@ class execution(_Config):
     """Run in sloppy mode (meaning, suboptimal parameters that minimize run-time)."""
     debug = []
     """Debug mode(s)."""
-    fmripost_aroma_dir = None
-    """Root of fMRIPost-AROMA BIDS Derivatives dataset. Depends on output_layout."""
     fs_license_file = _fs_license
     """An existing file containing a FreeSurfer license."""
     layout = None
@@ -451,7 +449,6 @@ class execution(_Config):
         'bids_dir',
         'derivatives',
         'bids_database_dir',
-        'fmripost_aroma_dir',
         'fs_license_file',
         'layout',
         'log_dir',

src/fmripost_aroma/data/tests/config.toml

@@ -18,7 +18,6 @@ log_level = 40
 low_mem = false
 md_only_boilerplate = false
 notrack = true
-fmripost_aroma_dir = "/home/runner/work/fmripost-aroma/fmripost-aroma/src/fmripost_aroma/tests/out"
 output_dir = "/home/runner/work/fmripost-aroma/fmripost-aroma/src/fmripost_aroma/tests/out"
 output_spaces = "MNI152NLin6Asym:res-2"
 reports_only = false

src/fmripost_aroma/tests/test_base.py

@@ -10,7 +10,7 @@ def test_init_ica_aroma_wf(tmp_path_factory):
     tempdir = tmp_path_factory.mktemp('test_init_ica_aroma_wf')
 
     with mock_config():
-        config.execution.fmripost_aroma_dir = tempdir / 'out'
+        config.execution.output_dir = tempdir / 'out'
         config.execution.work_dir = tempdir / 'work'
         config.workflow.denoise_method = ['nonaggr', 'orthaggr']
         config.workflow.melodic_dim = -200
@@ -29,7 +29,7 @@ def test_init_denoise_wf(tmp_path_factory):
     tempdir = tmp_path_factory.mktemp('test_init_denoise_wf')
 
     with mock_config():
-        config.execution.fmripost_aroma_dir = tempdir / 'out'
+        config.execution.output_dir = tempdir / 'out'
         config.execution.work_dir = tempdir / 'work'
 
         wf = init_denoise_wf(bold_file='sub-01_task-rest_bold.nii.gz')

src/fmripost_aroma/tests/tests.py

@@ -62,7 +62,7 @@ def mock_config():
     yield
 
     shutil.rmtree(config.execution.work_dir)
-    shutil.rmtree(config.execution.fmripost_aroma_dir)
+    shutil.rmtree(config.execution.output_dir)
 
     if not _old_fs:
         del os.environ['FREESURFER_HOME']

src/fmripost_aroma/workflows/aroma.py

@@ -260,7 +260,7 @@ def init_ica_aroma_wf(
 
     ds_report_ica_aroma = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='figures',
             desc='aroma',
@@ -291,7 +291,7 @@ def init_ica_aroma_wf(
 
     ds_components = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             compress=True,
             datatype='func',
@@ -312,7 +312,7 @@ def init_ica_aroma_wf(
 
     ds_mixing = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='func',
             res='2',
@@ -328,7 +328,7 @@ def init_ica_aroma_wf(
 
     ds_aroma_features = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='func',
             desc='aroma',
@@ -349,7 +349,7 @@ def init_ica_aroma_wf(
 
     ds_aroma_confounds = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='func',
             desc='melodic',
@@ -373,7 +373,7 @@ def init_ica_aroma_wf(
 
     ds_report_metrics = pe.Node(
         DerivativesDataSink(
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             source_file=bold_file,
             datatype='figures',
             desc='metrics',
@@ -456,7 +456,7 @@ def init_denoise_wf(bold_file):
 
         ds_denoised = pe.Node(
             DerivativesDataSink(
-                base_directory=config.execution.fmripost_aroma_dir,
+                base_directory=config.execution.output_dir,
                 source_file=bold_file,
                 compress=True,
                 datatype='func',

src/fmripost_aroma/workflows/base.py

@@ -72,7 +72,7 @@ def init_fmripost_aroma_wf():
         single_subject_wf = init_single_subject_wf(subject_id)
 
         single_subject_wf.config['execution']['crashdump_dir'] = str(
-            config.execution.fmripost_aroma_dir
+            config.execution.output_dir
             / f'sub-{subject_id}'
             / 'log'
             / config.execution.run_uuid
@@ -84,7 +84,7 @@ def init_fmripost_aroma_wf():
 
         # Dump a copy of the config file into the log directory
         log_dir = (
-            config.execution.fmripost_aroma_dir
+            config.execution.output_dir
             / f'sub-{subject_id}'
             / 'log'
             / config.execution.run_uuid
@@ -246,7 +246,7 @@ def init_single_subject_wf(subject_id: str):
     ds_report_summary = pe.Node(
         DerivativesDataSink(
             source_file=subject_data['bold'][0],
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             desc='summary',
             datatype='figures',
         ),
@@ -258,7 +258,7 @@ def init_single_subject_wf(subject_id: str):
     ds_report_about = pe.Node(
         DerivativesDataSink(
             source_file=subject_data['bold'][0],
-            base_directory=config.execution.fmripost_aroma_dir,
+            base_directory=config.execution.output_dir,
             desc='about',
             datatype='figures',
         ),